From kayttotuki at vtt.fi  Mon Mar  1 07:55:06 2004
From: kayttotuki at vtt.fi (kayttotuki at vtt.fi)
Date: Mon, 1 Mar 2004 14:55:06 +0200 (EET)
Subject: [EMBOSS] [#ID:71296#] Re: Document
In-Reply-To: <200403011253.i21CrM4v002570@mailgw.vtt.fi>
Message-ID: <4147547.1078145705781.JavaMail.SYSTEM@espsr05>

Kiitos. Viestisi on tallennettu ty?nhallintaj?rjestelm??mme.


From heltondz at artnet.com.br  Mon Mar  1 11:45:47 2004
From: heltondz at artnet.com.br (Ollie J. Helton)
Date: Mon, 01 Mar 2004 16:45:47 +0000
Subject: [EMBOSS] =?iso-8859-1?B?Q29zdGluZyB0byBtdWNoIGZvciB5b3UgUHJlc2NyaXAldGlvbiBEcil1Z3M/Pz8gQ2hlY2sgdGhpcyBvdXQh?=
Message-ID: <dba301c3ffac$cf31e8cc$39b5def1@8m4fph2>



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From BugEliminator at online-bargains01.com  Mon Mar  1 23:38:48 2004
From: BugEliminator at online-bargains01.com (Bug Eliminator)
Date: Tue, 02 Mar 2004 07:38:48 +0300
Subject: [EMBOSS] Complimentary Scan for your PC
Message-ID: <idg077Bidgfi1A0ut@online-bargains01.com>

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From didactic at itb.cnr.it  Tue Mar  2 10:17:34 2004
From: didactic at itb.cnr.it (didactic at itb.cnr.it)
Date: Tue, 02 Mar 2004 16:17:34 +0100
Subject: [EMBOSS] ello! =))
Message-ID: <suhvqdbshaaxdjttdkl@itb.cnr.it>

Looking forward for a response :P

68026  --  archive password
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From NAIILRIILRIKENX at ILRI.EXCH.CGIAR.ORG  Tue Mar  2 10:32:10 2004
From: NAIILRIILRIKENX at ILRI.EXCH.CGIAR.ORG (GroupShield for Exchange (ILRIKENX))
Date: Tue, 02 Mar 2004 07:32:10 -0800
Subject: [EMBOSS] ALERT -  GroupShield ticket number OA0_1078241530_ILRIKENX_1 was
	generated
Message-ID: <1F95CCD444D8D21180250090273F21FD069FC1AF@ILRIKENX>

Action Taken:
The attachment was deleted from the message and replaced with a text file
informing the recipient of the action taken.

To:
emboss at embnet.org <emboss at embnet.org>

From:
didactic at itb.cnr.it <didactic at itb.cnr.it>

Sent:
2095217408,29622377

Subject:
[EMBOSS] ello! =))

Attachment Details:-

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From support at embnet.org  Wed Mar  3 03:38:32 2004
From: support at embnet.org (support at embnet.org)
Date: Wed, 03 Mar 2004 18:38:32 +1000
Subject: [EMBOSS] E-mail account security warning.
Message-ID: <sdcryfrmevmjttrxdoy@embnet.org>

Dear user of Embnet.org gateway e-mail server,

Your e-mail  account has been temporary disabled because of  unauthorized access.

For  further details see  the attach.

Attached file protected with  the password for security  reasons. Password  is 11463.

The Management,
   The Embnet.org team                          http://www.embnet.org
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From siegmund at develogen.com  Thu Mar  4 05:42:34 2004
From: siegmund at develogen.com (Thomas Siegmund)
Date: Thu, 4 Mar 2004 11:42:34 +0100
Subject: [EMBOSS] Kaptain user interface, new release
Message-ID: <200403041142.34847.siegmund@develogen.com>

*This message was transferred with a trial version of CommuniGate(tm) Pro*
Hi everybody,

there is a new release of the EMBOSS.kaptn graphical user interface for EMBOSS 
running on Linux/X11 or MacOSX. Version 0.96 of the GUI is basically a bugfix 
release for use with EMBOSS 2.8.0.

Due to considerable efforts of the EMBOSS programmers towards a more 
consistent command line interface many emboss qualifiers have been changed or 
renamed during the last few EMBOSS releases. Unfortunately many of these 
changes were not listed in the EMBOSS ChangeLog. Therefore EMBOSS and the GUI 
have drifted apart to an unacceptable degree.

In order to fix this I made a little script to check the kaptain grammars 
against the acd files of a given EMBOSS release. I now have fixed all the 
problems shown by the script running against EMBOSS 2.8.0 . I'd recommend 
everybody using the Kaptain GUI with EMBOSS 2.8.0 to get the 0.96 version of 
the GUI. As you can see from the ChangeLog there were quite a few fixes to 
do :-0

Download, as usual, from 

http://userpage.fu-berlin.de/~sgmd/download.html

From the ChangeLog:

Version 0.96 - Use with EMBOSS 2.8
----------------------------------------------
- -startbase, -endbase, -separate for abiview.kaptn
- -aadata  for charge.kaptn
- -addlast , -report -> -outfile for checktrans.kaptn
- -sum for chips.kaptn
- -seqout -> -outseq in coderet.kaptn
- -obsexp, -cg, -pc and a new layout for cpgplot.kaptain
- small fix for cutgextract
- -aadata for digest.kaptn
- -maxrepeat for einverted
- -full for embossversion
- -nhydrophylic -> nohgap in emma.kaptn
- -onlydend for emma.kaptn
- -sequences -> -sequence in emowse.kaptn
- -aadata for emowse.kaptn
- removed -mmshow- -raccshow, and  -rdescshow from fuzznuc.kaptn,
  fuzzpro.kaptn, fuzztran.kaptn
- maxsize for getorf.kaptn
- -gi, -version for infoseq.kaptn
- -interticks for lindna.kapnt
- -outlist -> -outfile in listor.kaptn
- -report -> outfile in megamerger.kaptn
- -other -> -othersequence in merger.kaptn
- -showdel for mwfilter.kaptn
- -brief for needle.kaptn
- -sequencea -> -sequence in octanol.kaptn
- -insequence -> -sequence in palindrome.kaptn
- -sequence,-insseq -> -[ab]sequence
   and a cleaner layout for pasteseq.kaptn
- -insseq -> -sequence for pepinfo.kaptn
- -aadata for pepstats.kaptn
- -wheel for pepwheel.kaptn
- -msf -> -sequences for pepwindowall.kaptn
- -msf -> -sequences, remove -nodata in plotcon.kaptn
- -start, -stop for plotorf.kaptn
- -msf -> -sequences for prettyplot.kaptn
- -sequence -> -seqall for primersearch.kaptn
- added -name, -description, removed -preferred from remap.kaptn
- added -blunt, -sticky, removed -preferred from remap.kaptn
- added -datafile, removed -preferred from restrict.kaptn
- -feature for seqret.kaptn
- -strittags for showfeat.kaptn
- remove -preferred from showseq.kaptn
- -primers -> -primersfile, -sequences -> -seqall in stssearch.kaptn
- -msf -> -sequences in tmap.kaptn
- -nseq -> -asequence, -pseq -> -bsequence in tranalign.kaptn
- -feature for skipseq.kaptn
- -gapextend, -gapopen for supermatcher.kaptn
- -casesensitive for textsearch.kaptn (doesn't seem to work)
- -minlength, -custom for tfscan.kaptn
- -brief for water.kaptn
- added kaptncheck.pl, a quick hack to compare kaptain grammars
  with the acd files of a given EMBOSS release
- added sixpack.kaptn

Version 0.95 "Bangkok edition"
- remove -data in pepwheel.kapnt, pepnet.kaptn
- make -msf -sequence in all ephylip programms
- small fixes in needle.kaptn, water.kaptn

Version 0.94
- renamed pestfind.kaptn to epestfind.kaptn
- sequencea -> sequence in pepstats.kaptn
- rformat option for dreg.kaptn, preg.kaptn, recoder.kaptn, silent.kaptn

Regards,

Thomas

-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

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From acorbe2 at emory.edu  Thu Mar  4 11:03:12 2004
From: acorbe2 at emory.edu (Anita Corbett)
Date: Thu, 4 Mar 2004 11:03:12 -0500 (EST)
Subject: [EMBOSS] Out of Office
Message-ID: <200403041603.i24G3CKG002824@euphrosyne.cc.emory.edu>

I am out of the office until March 8, 2004.
Although I may have some e-mail access, it is likely that your mail regarding "Your bill." will be read when I return.
If you have something urgent, please contact someone in my lab (4158 RRC) at 404-727-4504.  Start with either Michelle (mtharre at emory.edu) or Sara (sleung at emory.edu).


From Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl  Fri Mar  5 06:19:20 2004
From: Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl (Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl)
Date: Fri, 05 Mar 2004 12:19:20 +0100
Subject: [EMBOSS] LUMC detected a problem with an email that appears to be received from you.
Message-ID: <20040305111921.4F73A7D0C9@mercury.hgmp.mrc.ac.uk>

The LUMC does not allow our users to receive
certain types of email.

In case of attachment blocking:
Your email is delivered to the recipient,
but attachment(s) have been removed.
Please place them in a ZIP file or send an URL to
the recipient to make them available for download.

In case of subject blocking:
Please rephrase your subject line.
Your email has NOT reached the intended recipient.

Please note that if you did not send a message to our recipient,
a number of computer viruses make it appear that the
author of a message is someone else.
If that's happened to you and you did not send the message
referred to below, please disregard this message.

From: emboss at embnet.org
To: j.a.maassen at lumc.nl

Subject: hello

Matching Subject: hello




From yann-francois.bizouerne at bayercropscience.com  Fri Mar  5 10:32:40 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Fri, 5 Mar 2004 16:32:40 +0100
Subject: [EMBOSS] question about "recoder" tool
Message-ID: <OFAC25D872.092BC3E7-ONC1256E4E.00551028-C1256E4E.00556389@bayer.de>





Hi,

I have the Emboss version  2.7.1 installed on our servers.
I try to execute the "recoder" tool as below.

   > recoder
   Remove restriction sites but maintain the same translation
   Nucleic acid sequence: seq.test
   Comma separated enzyme list [all]:
   Results file name [aa749534.recoder]:

      EMBOSS An error in recoder.c at line 380:
   Aborting...restriction file not found


It seems to not found the restriction file. Where can I get one ? And where put
it in Emboss directory ?

Thanks in advance


Yann-Fran?ois BIZOUERNE
BioInformatic Team
BAYER CropScience
4, rue Pierre Fontaine
91058 Evry Cedex
FRANCE
Phone:      33-(0) 1-69-47-61-56
FAX:        33-(0) 1-69-47-61-42
E-mail:     yann-francois.bizouerne at bayercropscience.com
Intranet: http://bioinfo.evry.fr.bayercropscience/



From gwilliam at hgmp.mrc.ac.uk  Fri Mar  5 10:39:31 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Fri, 05 Mar 2004 15:39:31 +0000
Subject: [EMBOSS] question about "recoder" tool
References: <OFAC25D872.092BC3E7-ONC1256E4E.00551028-C1256E4E.00556389@bayer.de>
Message-ID: <40489F33.6F2497BD@hgmp.mrc.ac.uk>


   This uses the EMBOSS REBASE data files in 'data/REBASE/*' under the
   EMBOSS installation directory.

   These files must first be set up using the program 'rebaseextract'.
   Running 'rebaseextract' may be the job of your system manager.

   See the documentation of rebaseextract for more details:
   http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/rebaseextract.html

Gary


yann-francois.bizouerne at bayercropscience.com wrote:
> 
> Hi,
> 
> I have the Emboss version  2.7.1 installed on our servers.
> I try to execute the "recoder" tool as below.
> 
>    > recoder
>    Remove restriction sites but maintain the same translation
>    Nucleic acid sequence: seq.test
>    Comma separated enzyme list [all]:
>    Results file name [aa749534.recoder]:
> 
>       EMBOSS An error in recoder.c at line 380:
>    Aborting...restriction file not found
> 
> It seems to not found the restriction file. Where can I get one ? And where put
> it in Emboss directory ?
> 
> Thanks in advance
> 
> Yann-Fran?ois BIZOUERNE
> BioInformatic Team
> BAYER CropScience
> 4, rue Pierre Fontaine
> 91058 Evry Cedex
> FRANCE
> Phone:      33-(0) 1-69-47-61-56
> FAX:        33-(0) 1-69-47-61-42
> E-mail:     yann-francois.bizouerne at bayercropscience.com
> Intranet: http://bioinfo.evry.fr.bayercropscience/

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From tchiang at bioinfo.sickkids.on.ca  Fri Mar  5 13:36:52 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Fri, 5 Mar 2004 13:36:52 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
Message-ID: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>


Hi,

I ran dbiflat on a swissprot flatfile with the option '-fields taxon' in
order to index the db by species.  All went well, and there were files:

taxon.hit
taxon.trg

produced in addition to the division.lkp and entrynam.idx.

My question is how do I now retrieve only the records that are for a given
species, ie.

$ entret swtest:HOMO
Reads and writes (returns) flatfiles entries
Error: Database Entry 'HOMO' not found
Error: Unable to read sequence 'swtest:HOMO'



I know the dbiflat worked, because when I run

$ entret swtest:*

I get all the files in the database.


Thanks for the help.



-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================




From jlaroche at bioinfo.ulaval.ca  Fri Mar  5 13:47:18 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Fri, 5 Mar 2004 13:47:18 -0500
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>
References: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>
Message-ID: <8748F918-6ED5-11D8-8A37-000A95CDA6C0@bioinfo.ulaval.ca>

Try this:

entret swtest-taxon:homo

If you want to use wildcard, you type :

entret swtest-taxon:homo\*


J?r?me

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-03-05, ? 13:36, Ted Chiang a ?crit :

>
> Hi,
>
> I ran dbiflat on a swissprot flatfile with the option '-fields taxon' 
> in
> order to index the db by species.  All went well, and there were files:
>
> taxon.hit
> taxon.trg
>
> produced in addition to the division.lkp and entrynam.idx.
>
> My question is how do I now retrieve only the records that are for a 
> given
> species, ie.
>
> $ entret swtest:HOMO
> Reads and writes (returns) flatfiles entries
> Error: Database Entry 'HOMO' not found
> Error: Unable to read sequence 'swtest:HOMO'
>
>
>
> I know the dbiflat worked, because when I run
>
> $ entret swtest:*
>
> I get all the files in the database.
>
>
> Thanks for the help.
>
>
>
> -Ted
>
>
> =====================================
> Ted Chiang, Analyst
> Centre for Computational Biology
> Hospital for Sick Children, Toronto
> 416.813.7028
> tchiang at bioinfo.sickkids.on.ca
> =====================================
>



From tchiang at bioinfo.sickkids.on.ca  Fri Mar  5 15:54:46 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Fri, 5 Mar 2004 15:54:46 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <8748F918-6ED5-11D8-8A37-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>


Thanks, but that doesn't seem to work.  Here is a record of what I did.


$dbiflat -fields=taxon
Index a flat file database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]:
Database directory [.]:
Wildcard database filename [*.dat]: *.test
Database name: swtest
Release number [0.0]:
Index date [00/00/00]:


$ls -l
-rw-r--r--           322 Mar  5 15:46 division.lkp
-rw-r--r--         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--       2081272 Mar  5 12:27 sw.test
-rw-r--r--         29176 Mar  5 15:46 taxon.hit
-rw-r--r--         64411 Mar  5 15:46 taxon.trg


$showdb -database swtest
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
swtest        P    OK  OK  OK  Swissprot indexed by field <taxon>


$entret swtest-taxon:homo\*
Reads and writes (returns) flatfile entries
Error: USA 'swtest-taxon:homo*' query field 'taxon' not defined for
database 'swtest'
Error: Unable to read sequence 'swtest-taxon:homo*'


$entret swtest:*
Reads and writes (returns) flatfile entries
Output file [hs11_arath.entret]: all_entries

$ls -l
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 15:51 all_entries
-rw-r--r--    1 tchiang  jamie           322 Mar  5 15:46 division.lkp
-rw-r--r--    1 tchiang  jamie         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 12:27 sw.test
-rw-r--r--    1 tchiang  jamie         29176 Mar  5 15:46 taxon.hit
-rw-r--r--    1 tchiang  jamie         64411 Mar  5 15:46 taxon.trg


----------------------------------------------


-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Fri, 5 Mar 2004, [ISO-8859-1] J?r?me Laroche wrote:

> Try this:
> 
> entret swtest-taxon:homo
> 
> If you want to use wildcard, you type :
> 
> entret swtest-taxon:homo\*
> 
> 
> J?r?me
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> Le 04-03-05, ? 13:36, Ted Chiang a ?crit :
> 
> >
> > Hi,
> >
> > I ran dbiflat on a swissprot flatfile with the option '-fields taxon' 
> > in
> > order to index the db by species.  All went well, and there were files:
> >
> > taxon.hit
> > taxon.trg
> >
> > produced in addition to the division.lkp and entrynam.idx.
> >
> > My question is how do I now retrieve only the records that are for a 
> > given
> > species, ie.
> >
> > $ entret swtest:HOMO
> > Reads and writes (returns) flatfiles entries
> > Error: Database Entry 'HOMO' not found
> > Error: Unable to read sequence 'swtest:HOMO'
> >
> >
> >
> > I know the dbiflat worked, because when I run
> >
> > $ entret swtest:*
> >
> > I get all the files in the database.
> >
> >
> > Thanks for the help.
> >
> >
> >
> > -Ted
> >
> >
> > =====================================
> > Ted Chiang, Analyst
> > Centre for Computational Biology
> > Hospital for Sick Children, Toronto
> > 416.813.7028
> > tchiang at bioinfo.sickkids.on.ca
> > =====================================
> >
> 
> 



From jlaroche at bioinfo.ulaval.ca  Sat Mar  6 14:49:03 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Sat, 6 Mar 2004 14:49:03 -0500
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>
References: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>
Message-ID: <52550CFD-6FA7-11D8-8A9B-000A95CDA6C0@bioinfo.ulaval.ca>

Hi Ted,

Try this:

1. dbiflat -fields taxon
choose the right format of your flatfile: entry format

2. Add the following lines in your .embossrc file:

DB swtest [
    type: N
    method: emblcd
    format: genbank <-specify the format
    dir: path    <- the path of your database
    indexdir: path   <-the path of your index files
    fields: org		<-the field you have indexed
]
3. seqret swtest-org:homo

I run a couple of test and it works. But you should knwo that not all 
words in the field  ORGANISM are indexed. Just those of taxonomic 
significance.

So in a genbank flatfile containing the following organism field for 
two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
viruses, no RNA stage' use together or alone were not recognized even 
if they are in the organism field.

   ORGANISM  Agrobacterium sp.
             Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
             Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
  or

   ORGANISM  Chlorella virus
             Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
Chlorovirus.



Good luck!


J?r?me
Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca


From yann-francois.bizouerne at bayercropscience.com  Mon Mar  8 02:28:54 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Mon, 8 Mar 2004 08:28:54 +0100
Subject: [EMBOSS] Need more info about REBASEEXTRACT
Message-ID: <OF09522F50.64983652-ONC1256E51.00281C58-C1256E51.0029195C@bayer.de>





Hello,

I try to use REBASEEXTRACT and I have the following error message

   > rebaseextract
   Extract data from REBASE
   Full pathname of WITHREFM file:
   /tools/bioinfo/app/Emboss/share/EMBOSS/data/REBASE/withrefm
   Full pathname of PROTO file:
   /tools/bioinfo/app/Emboss/share/EMBOSS/data/REBASE/proto

      EMBOSS An error in rebaseextract.c at line 161:
   Invalid withrefm file

I just donwload the last version of the withrefm and proto files from REBASE ftp
site (withrefm.403 & proto.403). I have rename these files as withrefm & proto
I have put these files in the path you can see above and I have run the
REBASEEXTRACT command.
Did I miss something ?



Yann BIZOUERNE




From yann-francois.bizouerne at bayercropscience.com  Mon Mar  8 03:30:58 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Mon, 8 Mar 2004 09:30:58 +0100
Subject: [EMBOSS] Please forget my precedent mail about REBASEEXTRACT. I found the solution
Message-ID: <OFB38A5D05.A509D0BC-ONC1256E51.002E99DD-C1256E51.002EC7E8@bayer.de>





I soluce my problem.
Sorry for the disturbance.



Yann BIZOUERNE



From isabelle.wells at Roche.COM  Mon Mar  8 04:06:04 2004
From: isabelle.wells at Roche.COM (Wells, Isabelle {PRBI~Basel})
Date: Mon, 08 Mar 2004 10:06:04 +0100
Subject: [EMBOSS] Problem with indexing of large files and seqret
Message-ID: <062896243F02D445AB77BD2B51E2F3730258AF@rbamsem3.emea.roche.com>

Hello all,

We have installed the emboss package 2.8.0 on both IRIX and Linux (64
bit) machines.  I have installed several databases, one of which is the
incremental updates of EMBL which we cumulate in a flat file now larger
than 2 GB. This database was successfully indexed using dbiflat, but we
have the problem that seqret either is enable to read a sequence and
dies or goes to a segmentation fault, depending on the position of the
sequence to read. 

I saw in the mailing list archives that this problem was already
mentioned in 2002, but is there now a way to solve it without splitting
the large flat file?

Thanks for your help,
Isabelle Wells

+--- O---O -------------------------------------------
      o-o         Isabelle Wells, Ph. D.
       O          Bioinformatics group
      o-o         F. Hoffmann-La Roche Ltd  
     o---o        PRBI-B, building 65/307
    o----o        CH-4070 Basel, Switzerland
   O----O         
   0--o           
     O	       
    o-o           E-mail: isabelle.wells at roche.com   
+- o---o ---------------------------------------------


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From David.Bauer at SCHERING.DE  Mon Mar  8 08:33:05 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Mon, 8 Mar 2004 14:33:05 +0100
Subject: [EMBOSS] staden gui
Message-ID: <OF5971F6E7.20C380B9-ONC1256E51.0049E191@schering.de>

Hello,

I have some problems getting the staden package installed.
All parts which do not use the iwidgets stuff are OK (gap4, trev).
But with spin, pregap4 etc. I'm getting the error messages below.
Any hints why the itcl3.3/itk3.3 part is not working ?

Thanks,
David.

> spin
unknown namespace in import pattern "itcl::*"
    while executing
"namespace import itcl::*"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/iwidgetsrc"
 line 12)
    invoked from within
"source
/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/iwidgetsrc"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list source $i]"
    (procedure "SetDefaults" line 42)
    invoked from within
"SetDefaults $tdir ${name}rc ${name}_defs"
    (procedure "simple_load_package" line 36)
    invoked from within
"simple_load_package $tcldir"
    (procedure "load_package" line 5)
    invoked from within
"load_package iwidgets"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/spinrc"
 line 8)
    invoked from within
"source
/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/spinrc"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list source $i]"
    (procedure "SetDefaults" line 42)
    invoked from within
"SetDefaults $tdir ${name}rc ${name}_defs"
    (procedure "simple_load_package" line 36)
    invoked from within
"simple_load_package $tcldir"
    (procedure "load_package" line 5)
    invoked from within
"load_package spin"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../lib/spin/spin.tcl"
 line 270)




From tchiang at bioinfo.sickkids.on.ca  Mon Mar  8 10:34:47 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Mon, 8 Mar 2004 10:34:47 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <52550CFD-6FA7-11D8-8A9B-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <Pine.GSO.4.05.10403081033590.9111-100000@kenny.bioinfo.sickkids.on.ca>

Jerome,

Thanks for your help.  Things seems to work pretty good.

-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Sat, 6 Mar 2004, [ISO-8859-1] J?r?me Laroche wrote:

> Hi Ted,
> 
> Try this:
> 
> 1. dbiflat -fields taxon
> choose the right format of your flatfile: entry format
> 
> 2. Add the following lines in your .embossrc file:
> 
> DB swtest [
>     type: N
>     method: emblcd
>     format: genbank <-specify the format
>     dir: path    <- the path of your database
>     indexdir: path   <-the path of your index files
>     fields: org		<-the field you have indexed
> ]
> 3. seqret swtest-org:homo
> 
> I run a couple of test and it works. But you should knwo that not all 
> words in the field  ORGANISM are indexed. Just those of taxonomic 
> significance.
> 
> So in a genbank flatfile containing the following organism field for 
> two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
> viruses, no RNA stage' use together or alone were not recognized even 
> if they are in the organism field.
> 
>    ORGANISM  Agrobacterium sp.
>              Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
>              Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
>   or
> 
>    ORGANISM  Chlorella virus
>              Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
> Chlorovirus.
> 
> 
> 
> Good luck!
> 
> 
> J?r?me
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> 



From louis at gtptech.com  Tue Mar  9 10:05:31 2004
From: louis at gtptech.com (Carole Louis)
Date: 09 Mar 2004 16:05:31 +0100
Subject: [EMBOSS] CUTG
Message-ID: <1078844731.3235.6.camel@Coriandre>

Hi,

I extracted the CUTG database with cutgextract without any problem but
I'd like to have a more explicite name for my .cut files ? Is it
possible to obtain it ?

Thanks,

-- 
Carole Louis <louis at gtptech.com>
GTP Technology
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From areagp61 at yahoo.it  Tue Mar  9 10:17:23 2004
From: areagp61 at yahoo.it (Graziano P.)
Date: Tue, 9 Mar 2004 16:17:23 +0100
Subject: [EMBOSS] CUTG
References: <1078844731.3235.6.camel@Coriandre>
Message-ID: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>

Hi Carol,
not every file but most are described in the README file from ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list I am using.

Regards
Graziano

Easn.cut  -  Aspergillus nidulans
Eath.cut  -  Arabidopsis thaliana
Ebly.cut  -  Hordeum vulgare (Barley)
Ebmo.cut  -  Bombyx mori (Silk Moth)
Ebov.cut  -  Bos taurus (Cow)
Ebsu.cut  -  Bacillus subtilis
Ecel.cut  -  Caenorhabditis elegans
Echi.cut  -  Chironomus sp.
Echk.cut  -  Gallus sp. (Chicken)
Eddi.cut  -  Dictyostelium discoideum
Edro.cut  -  Drosophila melanogaster
Eeco.cut  -  Escherichia coli
Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
Ehum.cut  -  Homo sapiens
Ekpn.cut  -  Klebsiella pneumoniae
Emac.cut  -  Macaca sp
Emus.cut  -  Mus sp. (Mouse)
Emze.cut  -  Zea mays (Maize)
Emzecp.cut  -  Zea mays chloroplast (Maize)
Eneu.cut  -  Neurospora crassa
Engo.cut  -  Neisseria gonorrheae
Epea.cut  -  Pisum sativum (Pea)
Epet.cut  -  Petunia sp.
Epfa.cut  -  Plasmodium falciparum
Ephv.cut  -  Phaseolus vulgaris (Lima bean)
Epot.cut  -  Solanum tuberosum (Pototoe)
Epse.cut  -  Pseudomonas sp.
Erab.cut  -  Oryctolagus sp. (Rabbit)
Erat.cut  -  Rattus sp. (Rat)
Erhm.cut  -  Rhizobium meliloti
Eric.cut  -  Oryza sativa (Rice)
Eshp.cut  -  Ovis sp. (Sheep)
Eslm.cut  -  Physarum polycephalum
Esoy.cut  -  Glycine max (Soybean)
Esta.cut  -  Staphylococcus aureus
Esty.cut  -  Salmonella thphimurium
Esus.cut  -  Strongylocentrotus purpuratus
Etob.cut  -  Nicotiana tabacum (Tobacco)
Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
Etom.cut  -  Lycopersicon esculentum (Tomato)
Etrb.cut  -  Trypanosoma brucei
Ewht.cut  -  Triticum aestivum (Wheat)
Exel.cut  -  Xenopus laevis
Eysc.cut  -  Saccharomyces cerevisiae
Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
Eysp.cut  -  Schizosaccharomyces pombe


----- Original Message ----- 
  From: Carole Louis 
  To: Liste Emboss 
  Sent: Tuesday, March 09, 2004 4:05 PM
  Subject: [EMBOSS] CUTG


  Hi,

  I extracted the CUTG database with cutgextract without any problem but I'd like to have a more explicite name for my .cut files ? Is it possible to obtain it ?

  Thanks,

        -- 
        Carole Louis <louis at gtptech.com>
        GTP Technology  
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From louis at gtptech.com  Wed Mar 10 03:31:23 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 09:31:23 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
Message-ID: <1078907483.3235.21.camel@Coriandre>

Thank you. I'm looking for Spodoptera frugiperda. I thought it was
Espo.cut but it seems very different of the table I found at
http://www.kazusa.or.jp/codon/. 


Le mar 09/03/2004 ? 16:17, Graziano P. a ?crit :

> ? 
> Hi Carol,
> not every file but most are described in the README file from
> ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list
> I am using.
>  
> Regards
> Graziano
>  
> Easn.cut  -  Aspergillus nidulans
> Eath.cut  -  Arabidopsis thaliana
> Ebly.cut  -  Hordeum vulgare (Barley)
> Ebmo.cut  -  Bombyx mori (Silk Moth)
> Ebov.cut  -  Bos taurus (Cow)
> Ebsu.cut  -  Bacillus subtilis
> Ecel.cut  -  Caenorhabditis elegans
> Echi.cut  -  Chironomus sp.
> Echk.cut  -  Gallus sp. (Chicken)
> Eddi.cut  -  Dictyostelium discoideum
> Edro.cut  -  Drosophila melanogaster
> Eeco.cut  -  Escherichia coli
> Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
> Ehum.cut  -  Homo sapiens
> Ekpn.cut  -  Klebsiella pneumoniae
> Emac.cut  -  Macaca sp
> Emus.cut  -  Mus sp. (Mouse)
> Emze.cut  -  Zea mays (Maize)
> Emzecp.cut  -  Zea mays chloroplast (Maize)
> Eneu.cut  -  Neurospora crassa
> Engo.cut  -  Neisseria gonorrheae
> Epea.cut  -  Pisum sativum (Pea)
> Epet.cut  -  Petunia sp.
> Epfa.cut  -  Plasmodium falciparum
> Ephv.cut  -  Phaseolus vulgaris (Lima bean)
> Epot.cut  -  Solanum tuberosum (Pototoe)
> Epse.cut  -  Pseudomonas sp.
> Erab.cut  -  Oryctolagus sp. (Rabbit)
> Erat.cut  -  Rattus sp. (Rat)
> Erhm.cut  -  Rhizobium meliloti
> Eric.cut  -  Oryza sativa (Rice)
> Eshp.cut  -  Ovis sp. (Sheep)
> Eslm.cut  -  Physarum polycephalum
> Esoy.cut  -  Glycine max (Soybean)
> Esta.cut  -  Staphylococcus aureus
> Esty.cut  -  Salmonella thphimurium
> Esus.cut  -  Strongylocentrotus purpuratus
> Etob.cut  -  Nicotiana tabacum (Tobacco)
> Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
> Etom.cut  -  Lycopersicon esculentum (Tomato)
> Etrb.cut  -  Trypanosoma brucei
> Ewht.cut  -  Triticum aestivum (Wheat)
> Exel.cut  -  Xenopus laevis
> Eysc.cut  -  Saccharomyces cerevisiae
> Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
> Eysp.cut  -  Schizosaccharomyces pombe
> 
>  
> ----- Original Message ----- 
> 
>         From: Carole Louis
>         To: Liste Emboss
>         Sent: Tuesday, March 09, 2004 4:05 PM
>         Subject: [EMBOSS] CUTG
>         
>         Hi,
>         
>         I extracted the CUTG database with cutgextract without any
>         problem but I'd like to have a more explicite name for my .cut
>         files ? Is it possible to obtain it ?
>         
>         Thanks,
>         
>         -- 
>         Carole Louis <louis at gtptech.com>
>         GTP Technology 

-- 
Carole Louis <louis at gtptech.com>
GTP Technology

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From louis at gtptech.com  Wed Mar 10 04:34:23 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 10:34:23 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
Message-ID: <1078911263.3235.33.camel@Coriandre>

Hi Graziano and thank you.

I'm looking for the table of Spodoptera frugiperda. I thought it was
Espo.cut but this table seems to be very different from that I found on
this internet site :   http://www.kazusa.or.jp/codon/.
Does anybody know which table is the one I need ?

Thanks,
Carole


Le mar 09/03/2004 ? 16:17, Graziano P. a ?crit :

> ? 
> Hi Carol,
> not every file but most are described in the README file from
> ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list
> I am using.
>  
> Regards
> Graziano
>  
> Easn.cut  -  Aspergillus nidulans
> Eath.cut  -  Arabidopsis thaliana
> Ebly.cut  -  Hordeum vulgare (Barley)
> Ebmo.cut  -  Bombyx mori (Silk Moth)
> Ebov.cut  -  Bos taurus (Cow)
> Ebsu.cut  -  Bacillus subtilis
> Ecel.cut  -  Caenorhabditis elegans
> Echi.cut  -  Chironomus sp.
> Echk.cut  -  Gallus sp. (Chicken)
> Eddi.cut  -  Dictyostelium discoideum
> Edro.cut  -  Drosophila melanogaster
> Eeco.cut  -  Escherichia coli
> Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
> Ehum.cut  -  Homo sapiens
> Ekpn.cut  -  Klebsiella pneumoniae
> Emac.cut  -  Macaca sp
> Emus.cut  -  Mus sp. (Mouse)
> Emze.cut  -  Zea mays (Maize)
> Emzecp.cut  -  Zea mays chloroplast (Maize)
> Eneu.cut  -  Neurospora crassa
> Engo.cut  -  Neisseria gonorrheae
> Epea.cut  -  Pisum sativum (Pea)
> Epet.cut  -  Petunia sp.
> Epfa.cut  -  Plasmodium falciparum
> Ephv.cut  -  Phaseolus vulgaris (Lima bean)
> Epot.cut  -  Solanum tuberosum (Pototoe)
> Epse.cut  -  Pseudomonas sp.
> Erab.cut  -  Oryctolagus sp. (Rabbit)
> Erat.cut  -  Rattus sp. (Rat)
> Erhm.cut  -  Rhizobium meliloti
> Eric.cut  -  Oryza sativa (Rice)
> Eshp.cut  -  Ovis sp. (Sheep)
> Eslm.cut  -  Physarum polycephalum
> Esoy.cut  -  Glycine max (Soybean)
> Esta.cut  -  Staphylococcus aureus
> Esty.cut  -  Salmonella thphimurium
> Esus.cut  -  Strongylocentrotus purpuratus
> Etob.cut  -  Nicotiana tabacum (Tobacco)
> Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
> Etom.cut  -  Lycopersicon esculentum (Tomato)
> Etrb.cut  -  Trypanosoma brucei
> Ewht.cut  -  Triticum aestivum (Wheat)
> Exel.cut  -  Xenopus laevis
> Eysc.cut  -  Saccharomyces cerevisiae
> Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
> Eysp.cut  -  Schizosaccharomyces pombe
> 
>  
> ----- Original Message ----- 
> 
>         From: Carole Louis
>         To: Liste Emboss
>         Sent: Tuesday, March 09, 2004 4:05 PM
>         Subject: [EMBOSS] CUTG
>         
>         Hi,
>         
>         I extracted the CUTG database with cutgextract without any
>         problem but I'd like to have a more explicite name for my .cut
>         files ? Is it possible to obtain it ?
>         
>         Thanks,
>         
>         -- 
>         Carole Louis <louis at gtptech.com>
>         GTP Technology 

-- 
Carole Louis <louis at gtptech.com>
GTP Technology

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From pmr at ebi.ac.uk  Wed Mar 10 04:29:16 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 10 Mar 2004 09:29:16 +0000
Subject: [EMBOSS] CUTG
In-Reply-To: <1078907483.3235.21.camel@Coriandre>
References: <1078844731.3235.6.camel@Coriandre>	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN> <1078907483.3235.21.camel@Coriandre>
Message-ID: <404EDFEC.1080407@ebi.ac.uk>

Carole Louis wrote:

> Thank you. I'm looking for Spodoptera frugiperda. I thought it was
> Espo.cut but it seems very different of the table I found at
> http://www.kazusa.or.jp/codon/. 

Spo.cut would be Schizosaccharomyces pombe.

After you run cutgextract on the cutg database from 
ftp.ebi.ac.uk/pub/databases/cutg you should have 
ESpodoptera_frugiperda.cut which comes from the gbinv.codons file.

The kazusa service looks interesting ... I wonder whether EMBOSS could 
read codon usage tables directly from there on request... I will try to 
make that work if there is enough interest.

>>----- Original Message ----- 
>>        From: Carole Louis
>>        To: Liste Emboss
>>        
>>        I extracted the CUTG database with cutgextract without any
>>        problem but I'd like to have a more explicite name for my .cut
>>        files ? Is it possible to obtain it ?

We are working on improving the naming and descriptions of codon usage 
files - for EMBOSS 2.9.0. This will have to include cutgextract output.

Does anyone need the codon usage files included in the EMBOSS 
distribution? We would like to "retire" the old ones (the long names) 
and rename (and update) the cutg ones.

regards,

Peter Rice



From louis at gtptech.com  Wed Mar 10 05:17:59 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 11:17:59 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <404EDFEC.1080407@ebi.ac.uk>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
	 <1078907483.3235.21.camel@Coriandre>  <404EDFEC.1080407@ebi.ac.uk>
Message-ID: <1078913877.3235.39.camel@Coriandre>

Thanks. I think it's a good idea to read codon usage tables directly on
kasuka website. 

Le mer 10/03/2004 ? 10:29, Peter Rice a ?crit :

> Carole Louis wrote:
> 
> > Thank you. I'm looking for Spodoptera frugiperda. I thought it was
> > Espo.cut but it seems very different of the table I found at
> > http://www.kazusa.or.jp/codon/. 
> 
> Spo.cut would be Schizosaccharomyces pombe.
> 
> After you run cutgextract on the cutg database from 
> ftp.ebi.ac.uk/pub/databases/cutg you should have 
> ESpodoptera_frugiperda.cut which comes from the gbinv.codons file.
> 
> The kazusa service looks interesting ... I wonder whether EMBOSS could 
> read codon usage tables directly from there on request... I will try to 
> make that work if there is enough interest.
> 
> >>----- Original Message ----- 
> >>        From: Carole Louis
> >>        To: Liste Emboss
> >>        
> >>        I extracted the CUTG database with cutgextract without any
> >>        problem but I'd like to have a more explicite name for my .cut
> >>        files ? Is it possible to obtain it ?
> 
> We are working on improving the naming and descriptions of codon usage 
> files - for EMBOSS 2.9.0. This will have to include cutgextract output.
> 
> Does anyone need the codon usage files included in the EMBOSS 
> distribution? We would like to "retire" the old ones (the long names) 
> and rename (and update) the cutg ones.
> 
> regards,
> 
> Peter Rice

-- 
Carole Louis <louis at gtptech.com>
GTP Technology
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From gbottu at ben.vub.ac.be  Wed Mar 10 05:46:29 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 10 Mar 2004 11:46:29 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <404EDFEC.1080407@ebi.ac.uk>
References: <1078844731.3235.6.camel@Coriandre> <010801c405e9$a23ea5b0$18105709@JTCDOMAIN> <1078907483.3235.21.camel@Coriandre> <404EDFEC.1080407@ebi.ac.uk>
Message-ID: <20040310104629.GB18868@bigben.ulb.ac.be>

On Wed, Mar 10, 2004 at 09:29:16AM +0000, Peter Rice wrote:
> We are working on improving the naming and descriptions of codon usage 
> files - for EMBOSS 2.9.0. This will have to include cutgextract output.
> 
> Does anyone need the codon usage files included in the EMBOSS 
> distribution? We would like to "retire" the old ones (the long names) 
> and rename (and update) the cutg ones.

Well, there are certainly a number of things that could be done to improve 
codon usage file support in EMBOSS. I would suggest :

- let any program that handles codon usage files read in user provided
files and/or write files in several formats (as is already done for
sequences and features) : CUTG, Staden, GCG, ... 
- for the EMBOSS included files : remove redundant files (why Eeco.cut and 
Eecoli.cut ?,...), provide clear information about which is which, 
update...
 - for CUTG, let cutgextract write file names based on the ID rather then 
the species name. This would provide names that are shorter and free from 
special characters.
- still for CUTG, a system to retrieve a file over the Internet from the 
distribution site is certainly interesting, but so is a way to retrieve it 
from a local SRS (with getz).
Note by the way that CUTG has a drawback : it has a table for each 
organism without making the distinction between different gene 
populations.

	Guy Bottu,
	Belgian EMBnet Node


From khoueiry at ibsm.cnrs-mrs.fr  Thu Mar 11 09:44:32 2004
From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre)
Date: Thu, 11 Mar 2004 15:44:32 +0100
Subject: [EMBOSS] uninstalling Emboss
Message-ID: <40507B50.204@ibsm.cnrs-mrs.fr>

Hi,
I want ot know the best way to uninstall Emboss from my Linux/Debian 
machine. In fact i install it using the tarball.
any suggesting thanks in advance
-- 

---------------------------------
Pierre Khoueiry	
khoueiry at ibsm.cnrs-mrs.fr
LCB - CNRS
31, Chemin Joseph Aiguier,
13402 Marseille CEDEX 20, France
---------------------------------




From kim at inb.uni-luebeck.de  Thu Mar 11 11:42:59 2004
From: kim at inb.uni-luebeck.de (Jan T. Kim)
Date: Thu, 11 Mar 2004 17:42:59 +0100
Subject: [EMBOSS] uninstalling Emboss
In-Reply-To: <40507B50.204@ibsm.cnrs-mrs.fr>; from khoueiry@ibsm.cnrs-mrs.fr on Thu, Mar 11, 2004 at 03:44:32PM +0100
References: <40507B50.204@ibsm.cnrs-mrs.fr>
Message-ID: <20040311174258.E17507@pc10.inb.mu-luebeck.de>

On Thu, Mar 11, 2004 at 03:44:32PM +0100, KHOUEIRY pierre wrote:

> I want ot know the best way to uninstall Emboss from my Linux/Debian 
> machine. In fact i install it using the tarball.
> any suggesting thanks in advance

Since the make process of the EMBOSS package is built with the autoconf
and automake standard tool suite, there is an uninstall target which
you can use for uninstalling. I.e. go to the EMBOSS source directory
where you ran ``make install'', and run ``make uninstall'' there.
If you don't have that source directory anymore, you could unpack the
tarball once more and run the ./configure script with exactly the
same parameters as you did for installing.

Greetinx, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: kim at inb.uni-luebeck.de                          |
 |    *NEW*    WWW:   http://www.inb.uni-luebeck.de/staff/kim.html    |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*


From Paul.Baumgartner at unibas.ch  Thu Mar 11 11:48:04 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Thu, 11 Mar 2004 17:48:04 +0100
Subject: [EMBOSS] MacOSXPanther
Message-ID: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>

During compilation of emboss 2.8.0-2 the process stopped with this 
comment :
......................
checking if java include directory given... yes
Java directory /Library/Java/Home exists
checking for javac... yes
checking if java OS include directory given... yes
Javaos directory /Library/Java/Home/include does not exist
make
make: *** No targets specified and no makefile found.  Stop.
### execution of make failed, exit code 2
Failed: compiling emboss-2.8.0-2 failed

a problem by Java ?

(all other packages (e.g. rasmol) compiled perfect)
Thanks to suggestions
Paul



From ableasby at hgmp.mrc.ac.uk  Thu Mar 11 13:14:35 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Thu, 11 Mar 2004 18:14:35 GMT
Subject: [EMBOSS] MacOSXPanther
Message-ID: <200403111814.i2BIEZHg017285@bromine.hgmp.mrc.ac.uk>

The SDK component of Java isn't installed from the CD by default.
It is on your 3rd Panther CD though.

HTH

Alan Bleasby
RFCGR


From kvddrift at earthlink.net  Thu Mar 11 17:56:06 2004
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 11 Mar 2004 17:56:06 -0500
Subject: [EMBOSS] MacOSXPanther
In-Reply-To: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>
References: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>
Message-ID: <47756100-73AF-11D8-A878-003065A5FDCC@earthlink.net>


On Mar 11, 2004, at 11:48 AM, Paul Baumgartner wrote:

> a problem by Java ?
>
> (all other packages (e.g. rasmol) compiled perfect)
> Thanks to suggestions
>

You need to install the Java SDK, this is not installed by default. See 
the fink website (fink.sf.net).


- Koen.



From fernan at iib.unsam.edu.ar  Mon Mar 15 11:51:05 2004
From: fernan at iib.unsam.edu.ar (Fernan Aguero)
Date: Mon, 15 Mar 2004 13:51:05 -0300
Subject: [EMBOSS] Bug in fuzznuc output?
Message-ID: <20040315165105.GD45860@iib.unsam.edu.ar>

Hi!

I'm searching for a nucleic acid pattern in a set of
sequences. The sequences are in a multiple fasta file, and
I'm searching for the pattern in both strands.

While testing my searches and adjusting the number of
mismatches that I would allow, I noticed that in the
standard output format, if the pattern matches in the
reverse strand, then Start > End (i.e. the position in the
sequence where the pattern begins is given with respect to
the plus strand).

Now, for my work I need to have the output in an easy to
parse format. But if I choose to have the output in
tab-delimited form (-rformat excel), then the Start and End
positions are always (i.e. in all cases) shown with Start <
End. Thus, there is no way to tell which are the cases of
matches to the reverse strand.

Is this an already known issue?

Since we are already here, let's go for a few suggestions:
in the standard output format (seqtable), there is a header
which includes the program, rundate, report format, etc. It
seems to me that this header is there to summarize global
info about the fuzznuc run.

Then, for each sequence analyzed the report shows the
pattern, the number of mismatches allowed, the number of
hits, and whether or not the complementary strand has been
searched. At least for me, there is unnecessary repetition.

For example: in all cases we have look for the same pattern,
allowing for the same number of mismatches and asking to
search also on the reverse strand. So why not put these
runtime values in the header, and avoid the repetition?

Also, why not report if the match was on the forward or
reverse strand _for each sequence_? (I mean, to make it more
clear, and not just let the user note that Start > End).

Thanks in advance,

Fernan

PS: BTW, I'm running EMBOSS-2.6.0 on FreeBSD-4.9

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan


From stefanie.debodt at psb.ugent.be  Tue Mar 16 12:51:00 2004
From: stefanie.debodt at psb.ugent.be (Stefanie De Bodt)
Date: Tue, 16 Mar 2004 18:51:00 +0100
Subject: [EMBOSS] seqret
Message-ID: <40573E84.4050305@psb.ugent.be>

Dear,

I am using the EMBOSS program SEQRET to retrieve sequences in EMBL 
format out a local EMBL database. Retrieving embl formatted sequences 
works. On your web site, I found an option, -feature, which allows 
additional information to be included in the embl result file. This 
however didn?t work, not in interactive mode and not using the following 
command line

seqret -feature -sequence DBname:AC -outseq embl:AC.embl

I get several warnings and I can?t figure out what the reason for these 
warnings is.

Warning: bad /cons_splice value '(5'site:YES,'
Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'
Warning: RICAMYBA: Bad value '(5'site:no,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'
Warning: RICAMYBB: Bad value '(5'site:no,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'

Could you help me with this problem, is there a mistake in the command 
line or is it due to something else?

Best regards,

Stefanie De Bodt

-- 
Stefanie De Bodt
Research Group of Bioinformatics and Evolutionary Genomics
Department of Plant Systems Biology
Ghent University - Flemish Institute for Biotechnology (VIB)
Technologiepark 927, B-9052 Ghent, BELGIUM

Tel: +32 (0)9 3313692
Fax: +32 (0)9 3313809

stefanie.debodt at psb.ugent.be
http://www.psb.ugent.be/bioinformatics




From pmr at ebi.ac.uk  Tue Mar 16 13:05:50 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 16 Mar 2004 18:05:50 +0000
Subject: [EMBOSS] seqret
In-Reply-To: <40573E84.4050305@psb.ugent.be>
References: <40573E84.4050305@psb.ugent.be>
Message-ID: <405741FE.4020000@ebi.ac.uk>

Stefanie De Bodt wrote:

> seqret -feature -sequence DBname:AC -outseq embl:AC.embl
> 
> I get several warnings and I can?t figure out what the reason for these 
> warnings is.
> 
> Warning: bad /cons_splice value '(5'site:YES,'
> Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
> 
> Could you help me with this problem, is there a mistake in the command 
> line or is it due to something else?

EMBOSS validates the EMBL feature table syntax, using a reasonably 
up-to-date version of the EMBL feature table document (I do have some 
minor updates to add for the latest version).

Is this your own database, or is this an EMBL entry?

These are only warnings ... but I would be interested to see the output 
of entret (the complete text of the entry as read by EMBOSS) to check 
the feature validation is correct.

regards,

Peter Rice



From stefanie.debodt at psb.ugent.be  Tue Mar 16 13:21:16 2004
From: stefanie.debodt at psb.ugent.be (Stefanie De Bodt)
Date: Tue, 16 Mar 2004 19:21:16 +0100
Subject: [EMBOSS] seqret
In-Reply-To: <405741FE.4020000@ebi.ac.uk>
References: <40573E84.4050305@psb.ugent.be> <405741FE.4020000@ebi.ac.uk>
Message-ID: <4057459C.1090303@psb.ugent.be>



Peter Rice wrote:

> Stefanie De Bodt wrote:
>
>> seqret -feature -sequence DBname:AC -outseq embl:AC.embl
>>
>> I get several warnings and I can?t figure out what the reason for 
>> these warnings is.
>>
>> Warning: bad /cons_splice value '(5'site:YES,'
>> Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
>>
>> Could you help me with this problem, is there a mistake in the 
>> command line or is it due to something else?
>
>
> EMBOSS validates the EMBL feature table syntax, using a reasonably 
> up-to-date version of the EMBL feature table document (I do have some 
> minor updates to add for the latest version).
>
> Is this your own database, or is this an EMBL entry?

I downloaded the database just recently from the NCBI FTP site. It is 
the database that contains all plant nucleotide sequences.

>
> These are only warnings ... but I would be interested to see the 
> output of entret (the complete text of the entry as read by EMBOSS) to 
> check the feature validation is correct.

Indeed, only warnings.The output file seems OK. I have attached it.

thanks,

Stefanie De Bodt

>
> regards,
>
> Peter Rice
>
>

-- 
Stefanie De Bodt
Research Group of Bioinformatics and Evolutionary Genomics
Department of Plant Systems Biology
Ghent University - Flemish Institute for Biotechnology (VIB)
Technologiepark 927, B-9052 Ghent, BELGIUM

Tel: +32 (0)9 3313692
Fax: +32 (0)9 3313809

stefanie.debodt at psb.ugent.be
http://www.psb.ugent.be/bioinformatics

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From EliminateBugs at bestholidaygifts01.com  Tue Mar 16 13:50:22 2004
From: EliminateBugs at bestholidaygifts01.com (CarsAmerica.com)
Date: Tue, 16 Mar 2004 21:50:22 +0300
Subject: [EMBOSS] Want a New Car?
Message-ID: <idg077Bidgfi1A0ut@bestholidaygifts01.com>

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From d.gatherer at vir.gla.ac.uk  Wed Mar 17 11:34:31 2004
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Wed, 17 Mar 2004 16:34:31 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <5.2.1.1.1.20030930111106.00b14960@udcf.gla.ac.uk>
Message-ID: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>

Hi

Is there an esim4 man page?

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html

The rest of EMBASSY is above, but not esim4.  The original sim4 has a quick 
help list, but I wondered if there is any extra functionality in the 
EMBASSY version.

Cheers
Derek

 > sim4
sim4 seq1 seq2_db [[WXKCRDHAPNBS]=]

        W  -  word size. (W=12)
        X  -  value for terminating word extensions. (X=12)
        K  -  MSP score threshold for the first pass. (e.g., K=16)
        C  -  MSP score threshold for the second pass. (e.g., C=12)
        R  -  direction of search; 0 - search the '+' (direct) strand only;
              1 - search the '-' strand only; 2 - search both strands and
              report the best match. (R=2)
        D  -  bound for the range of diagonals within consecutive msps in an
              exon. (D=10)
        H  -  weight factor for MSP scores in relinking. (H=500)
        A  -  output format: exon endpoints only (A=0), alignment text (A=1),
              alignment in lav (block) format (A=2), or both exon endpoints
              and alignment text (A=3, A=4). If complement match, A=0,1,2,3
              give direct positions in the long sequence and complement
              positions in the short sequence. A=4 gives direct positions in
              the first sequence, regardless of the relative lengths.
              A=5 prints the exon and CDS coordinates (the latter, if known)
              in the `exon file' format required by PipMaker. To be used
              with full-length mRNA sequences.
        P  -  if not 0, remove poly-A tails; report coordinates in the
              '+' (direct) strand for complement matches; use lav alignment
              headers in all display options. (P=0)
        N  -  accuracy of sequences (non-zero for highly accurate). (N=0)
        B  -  if 0, dis-allow ambiguity codes (other than N and X) in the
              sequence data. (B=1)
        S  -  coding region specification (available only with A=5);
              format: S=n1..n2



From mathog at mendel.bio.caltech.edu  Wed Mar 17 11:44:03 2004
From: mathog at mendel.bio.caltech.edu (David Mathog)
Date: Wed, 17 Mar 2004 08:44:03 -0800
Subject: [EMBOSS] esim4 man page
Message-ID: <E1B3e9D-0001qC-00@mendel.bio.caltech.edu>

> Is there an esim4 man page?

I don't recall writing one.  esim4 -h will list the command line
options and what they do, to the extent that could be decipered
from the original source code.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From d.m.a.martin at dundee.ac.uk  Wed Mar 17 12:03:06 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 17 Mar 2004 17:03:06 +0000
Subject: [EMBOSS] Problems retrieving from uniprot by id
Message-ID: <BC7E354A.FF39%d.m.a.martin@dundee.ac.uk>

Using EMBOSS 2.8.0 I am trying to retrieve from Uniprot by ID without
success. This is using the Swissprot

I have indexed appropriately ( using fields as described on the emboss
documentation.)

I can retrieve by accession number but cannot retrieve the same sequence by
id. 

I have run the program with -debug and get the following:

ajFileNewIn '/mn/proteas/u1/davidm/entrynam.idx'
seqCdReadHeader file /mn/proteas/u1/davidm/entrynam.idx
  FileSize: 2912040 NRecords: 145587 recsize: 20 idsize: 10
seqCdFileOpen '/mn/proteas/u1/davidm/entrynam.idx' NRecords: 145587 RecSize:
20
entry id: 'tf_human' acc: ''
entry id: 'tf_human' acc: ''
seqCdIdxSearch (entry 'tfz_human') records: 145587
idx test 72793 'NUYM_HUMAN'  1 (+/- 145586)
idx test 109190 'SYFA_SULTO'  1 (+/- 72792)
idx test 127388 'Y06C_BPT4' -1 (+/- 36395)
idx test 118289 'UAP1_ARATH' -1 (+/- 18196)
idx test 113739 'THS1_ARAHY' -1 (+/- 9097)
idx test 111464 'TAR5_HUMAN'  1 (+/- 4547)
idx test 112601 'TERT_OXYTR'  1 (+/- 2273)
idx test 113170 'THI1_CORNE' -1 (+/- 1136)
idx test 112885 'TGF2_RAT' -1 (+/- 567)
idx test 112743 'TFB1_THEVO'  1 (+/- 282)
idx test 112814 'TFPI_HUMAN'  1 (+/- 140)
idx test 112849 'TFZ_DROME'  1 (+/- 69)
idx test 112867 'TGF1_BOVIN' -1 (+/- 34)
idx test 112858 'TGA5_ARATH' -1 (+/- 16)
idx test 112853 'TG37_MOUSE' -1 (+/- 7)
idx test 112851 'TG21_TOBAC' -1 (+/- 2)
idx test 112850 'TFZ_HUMAN'  0 (+/- 0)
EMBLCD Entry failed
Database Entry 'tf_human' not found
seqCdQryClose clean up qryd
seqCdFileClose of /mn/proteas/u1/davidm/entrynam.idx
closing file '/mn/proteas/u1/davidm/entrynam.idx'
seqCdFileClose of /mn/proteas/u1/davidm/division.lkp
closing file '/mn/proteas/u1/davidm/division.lkp'
Database 'sw' : access method 'emblcd' failed

It might be an 'off by one' error in the  search or the indexing.
searching for tfz_human behaves appropriately.

..d

-- 
David Martin PhD <david at compbio.dundee.ac.uk>
Post-Genomics and Molecular Interactions Centre
University of Dundee




From EliminateBugs at special-deal0001.com  Wed Mar 17 19:22:27 2004
From: EliminateBugs at special-deal0001.com (Reduce Body Fat)
Date: Thu, 18 Mar 2004 03:22:27 +0300
Subject: [EMBOSS] Accelerate Weight Loss
Message-ID: <idg077Bidgfi1A0ut@special-deal0001.com>

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From stefanielager at fastmail.ca  Thu Mar 18 01:08:45 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 18 Mar 2004 06:08:45 +0000 (UTC)
Subject: [EMBOSS] esim4 man page
In-Reply-To: <E1B3e9D-0001qC-00@mendel.bio.caltech.edu>
Message-ID: <20040318060846.CB20C861C92@mail.interchange.ca>

ESIM4 doesn't seem to be able to align multiple mRNA sequences to a
single genomic sequence, which sim4 as an external program can. In
version 2.8.0 of emboss ESIM4 alignments don't work (format=3), it finds
the correct reagion to align, but it seems to "extract" the wrong
genomic region to make the alignment (it was OK in version 2.6.0 of
EMBOSS). 

Stefanie

>> Is there an esim4 man page?
> 
> I don't recall writing one.  esim4 -h will list the command line
> options and what they do, to the extent that could be decipered
> from the original source code.
> 
> Regards,
> 
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From pmr at ebi.ac.uk  Thu Mar 18 05:06:41 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Mar 2004 10:06:41 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <20040318060846.CB20C861C92@mail.interchange.ca>
References: <20040318060846.CB20C861C92@mail.interchange.ca>
Message-ID: <405974B1.8070507@ebi.ac.uk>

Stefanie Lager wrote:

> ESIM4 doesn't seem to be able to align multiple mRNA sequences to a
> single genomic sequence, which sim4 as an external program can. In
> version 2.8.0 of emboss ESIM4 alignments don't work (format=3), it finds
> the correct reagion to align, but it seems to "extract" the wrong
> genomic region to make the alignment (it was OK in version 2.6.0 of
> EMBOSS). 

Thanks for pointing that out.

I am working on QA tests for the EMBASSY programs and will put these 
test cases in.

regards,

Peter Rice



From pmr at ebi.ac.uk  Thu Mar 18 05:05:28 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Mar 2004 10:05:28 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>
References: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>
Message-ID: <40597468.2000801@ebi.ac.uk>

Derek Gatherer wrote:

> Hi
> 
> Is there an esim4 man page?
> 
> http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html
> 
> The rest of EMBASSY is above, but not esim4.  The original sim4 has a 
> quick help list, but I wondered if there is any extra functionality in 
> the EMBASSY version.

As it happens, I am working through the EMBASSY programs that don't have 
man pages - hmmer is also missing.

They will appear soon.

regards,

Peter Rice



From sandeepd at persistent.co.in  Thu Mar 18 08:18:06 2004
From: sandeepd at persistent.co.in (sandeepd at persistent.co.in)
Date: Thu, 18 Mar 2004 18:48:06 +0530
Subject: [EMBOSS] Blocked delivery of your email to chitra@pspl.co.in
Message-ID: <200403181318.i2IDI8VK008989@smtp.pspl.co.in>

                 BLOCKED DELIVERY OF YOUR EMAIL TO chitra at pspl.co.in 

Your email has been stopped for reasons stated at the bottom of this mail.

If your message is HTML/RichText and wrongly reported as SPAM below 
send the email again in plain-text format. 

If your message is reported to have virus, please check your system 
for virii and clean it up. 

If you still think that your message is free of all the above, please 
report it to postmaster at persistent.co.in or sysads at persistent.co.in. 


Email was blocked due to the presence of a virus
	Comment: Virus detected in the mail

/unpacked/mp3music.pif - Win32/Netsky.D worm


End.


From LendersCompete at bargains001.com  Sat Mar 20 07:38:58 2004
From: LendersCompete at bargains001.com (Lenders Compete)
Date: Sat, 20 Mar 2004 15:38:58 +0300
Subject: [EMBOSS] Low Rates, Trusted Lenders
Message-ID: <idg077Bidgfi1A0ut@bargains001.com>

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From antivirus at unito.it  Sat Mar 20 09:28:37 2004
From: antivirus at unito.it (antivirus at unito.it)
Date: Sat, 20 Mar 2004 15:28:37 +0100
Subject: [EMBOSS] - DO NOT REPLY - Inflex scan report [0320152824368]
Message-ID: <200403201428.i2KESb7j024400@albert.unito.it>

Administrator Email Reply Address: rete at unito.it
Email sent to:  sergio.castellano at unito.it
Inflex ID: 0320152824368
Report Details -----------------------------------------------
AntiVirus Results...

File NAME/TYPE Scan Results
 MS-DOS executable (EXE), OS/2 or MS Windows


0320152824368  from:emboss at embnet.org  to: sergio.castellano at unito.it
END OF MESSAGE.

End.
.


From georg.otto at tuebingen.mpg.de  Mon Mar 22 16:34:58 2004
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Mon, 22 Mar 2004 22:34:58 +0100
Subject: [EMBOSS] eprimer3
Message-ID: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>

Hi,

I have problems using eprimer3. It seems to me that it can?t take 
multiple sequence files as an input (I tried with a multiple fasta file 
and a file in EMBL format). However primer3 itself can take multiple 
sequences. Is there something I missed?

Best regards,

Georg


From stefanielager at fastmail.ca  Tue Mar 23 01:53:52 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Tue, 23 Mar 2004 06:53:52 +0000 (UTC)
Subject: [EMBOSS] eprimer3
Message-ID: <20040323065416.8A9D8865D28@mail.interchange.ca>

I haven?t used eprimer3 extensively, but for version 2.8.0 of EMBOSS
eprimer3 can take multiple fasta sequence files as input, and it designs
primers for all input sequences.

Stefanie

> Hi,
> 
> I have problems using eprimer3. It seems to me that it can?t take
> multiple sequence files as an input (I tried with a multiple fasta
> file and a file in EMBL format). However primer3 itself can take
> multiple sequences. Is there something I missed?
> 
> Best regards,
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From henrikki.almusa at helsinki.fi  Tue Mar 23 02:15:04 2004
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Tue, 23 Mar 2004 09:15:04 +0200
Subject: [EMBOSS] eprimer3
In-Reply-To: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>
References: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>
Message-ID: <200403230915.04470.henrikki.almusa@helsinki.fi>

On Monday 22 March 2004 23:34, Georg Otto wrote:
> Hi,
>
> I have problems using eprimer3. It seems to me that it can?t take
> multiple sequence files as an input (I tried with a multiple fasta file
> and a file in EMBL format). However primer3 itself can take multiple
> sequences. Is there something I missed?

Mail from archives:

----

[EMBOSS] eprimer3: max input file number?
Date: 21.10.2003 19:41
From: Iain Drummond <idrummon at receptor.mgh.harvard.edu>

I have run into a limitation using eprimer3 as an interface for primer3. It
seems that eprimer3 will accept up to 23 sequences (in a single fasta
formatted text file) but not 24 or more; with 24 or more sequences, eprimer3
and primer3_core will just hang as ?sleeping? processes and never finish. My
goal is to automate genomic sequence analysis (zebrafish) in order to
generate new, potentially useful polymorphic markers from dinucleotide
repeats. eprimer3 is the last step where a long list of ~500 bp sequences
are sent to primer3 to make primers.

-----

And reply to above:

-----

Re: [EMBOSS] maximum number of sequences for eprimer3
Date: 22.10.2003 22:06
From: Alan Bleasby <ableasby at hgmp.mrc.ac.uk>

Having had a quick look at the code I suspect that it is not
a variable involved (EMBOSS programs are designed not to be
limited in that way, usually only by system resource available).
 
The code uses pipes to redirect stdin and stdout to/from primer3_core.
A possible cause is therefore blocking from a full buffer. I'll
let the author of the eprimer3 program know about it.

HTH

Alan

----

-- 
Henrikki Almusa


From pscotney at hotmail.com  Tue Mar 23 02:16:41 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Tue, 23 Mar 2004 18:16:41 +1100
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
Message-ID: <Sea2-F29qNHKEn8diHN0000c39a@hotmail.com>


Hello,

I am having problems installing EMBOSS and Jemboss.  I have read all the 
INSTALL and README docs in the EMBOSS-2.8.0 directory and the web docs for 
Jemboss standalone installation, so please no RTFM responses :)

I am building EMBOSS-2.8.0 on a GNU/Linux system (Mandrake 9.1) with 
Blackdown Java j2sdk-1.3.1-02b-FCS-linux-i386 installed and running ok.  I 
have installed zlib-1.2.1 libpng-1.2.5 and gd-2.0.22 so all the libraries 
and includes are present.

I build as root with the following commands:

cd EMBOSS-2.8.0
./configure --prefix=/usr/local/emboss
make
make install
cd jemboss/utils
./install-jemboss-server.sh

selecting the option (2) STANDALONE and the rest of the prompts.  The 
generated /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh and 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties files 
all look ok with the correct paths.

I have added /usr/local/emboss/{bin,lib} to the PATH and ld.so.conf 
respectively and wosname -auto is working:

ALIGNMENT CONSENSUS
cons             Creates a consensus from multiple alignments
megamerger       Merge two large overlapping nucleic acid sequences
merger           Merge two overlapping nucleic acid sequences
etc.....

but when I

cd /usr/local/emboss/share/EMBOSS/jemboss
./runJemboss.sh

all I ever get is the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: 
org/emboss/jemboss/Jemboss

What have I done wrong?  Please help!

Regards

Pierre


--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
SEEK: Now with over 50,000 dream jobs! Click here:  
http://ninemsn.seek.com.au?hotmail



From tcarver at rfcgr.mrc.ac.uk  Tue Mar 23 03:26:07 2004
From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver)
Date: Tue, 23 Mar 2004 08:26:07 +0000 (GMT)
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
In-Reply-To: <Sea2-F29qNHKEn8diHN0000c39a@hotmail.com>
Message-ID: <Pine.SOL.4.44.0403230823410.5931-100000@uranium>

Hi Pierre

The problem is likely to be that you precompiled emboss before running
the install script. There is no need, the install script does this for
you with the correct java flags. Try a 'make clean' and then run the
install script.

Hope this helps.
Regards
Tim Carver

RFCGR

>
> I am building EMBOSS-2.8.0 on a GNU/Linux system (Mandrake 9.1) with
> Blackdown Java j2sdk-1.3.1-02b-FCS-linux-i386 installed and running ok.  I
> have installed zlib-1.2.1 libpng-1.2.5 and gd-2.0.22 so all the libraries
> and includes are present.
>
> I build as root with the following commands:
>
> cd EMBOSS-2.8.0
> ./configure --prefix=/usr/local/emboss
> make
> make install
> cd jemboss/utils
> ./install-jemboss-server.sh
>
> selecting the option (2) STANDALONE and the rest of the prompts.  The
> generated /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh and
> /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties files
> all look ok with the correct paths.
>
> I have added /usr/local/emboss/{bin,lib} to the PATH and ld.so.conf
> respectively and wosname -auto is working:
>
> ALIGNMENT CONSENSUS
> cons             Creates a consensus from multiple alignments
> megamerger       Merge two large overlapping nucleic acid sequences
> merger           Merge two overlapping nucleic acid sequences
> etc.....
>
> but when I
>
> cd /usr/local/emboss/share/EMBOSS/jemboss
> ./runJemboss.sh
>
> all I ever get is the following error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/emboss/jemboss/Jemboss
>
> What have I done wrong?  Please help!
>
> Regards
>
> Pierre
>
>
> --
> Dr Pierre Scotney
> Melbourne
> Australia
>
> _________________________________________________________________
> SEEK: Now with over 50,000 dream jobs! Click here:
> http://ninemsn.seek.com.au?hotmail
>



From gwilliam at hgmp.mrc.ac.uk  Tue Mar 23 04:27:58 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 23 Mar 2004 09:27:58 +0000
Subject: [EMBOSS] eprimer3
References: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de> <200403230915.04470.henrikki.almusa@helsinki.fi>
Message-ID: <4060031D.E530E8C9@hgmp.mrc.ac.uk>


The 23 input sequence limitation of eprimer3 will be fixed in the next
release.
In the meantime, you could get a copy of the fixed program from:
ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/eprimer3.*

Regards,
Gary

Henrikki Almusa wrote:
> [EMBOSS] eprimer3: max input file number?
> Date: 21.10.2003 19:41
> From: Iain Drummond <idrummon at receptor.mgh.harvard.edu>
> 
> I have run into a limitation using eprimer3 as an interface for primer3. It
> seems that eprimer3 will accept up to 23 sequences (in a single fasta
> formatted text file) but not 24 or more; with 24 or more sequences, eprimer3
> and primer3_core will just hang as ?sleeping? processes and never finish. My
> goal is to automate genomic sequence analysis (zebrafish) in order to
> generate new, potentially useful polymorphic markers from dinucleotide
> repeats. eprimer3 is the last step where a long list of ~500 bp sequences
> are sent to primer3 to make primers.


-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pscotney at hotmail.com  Tue Mar 23 23:13:01 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Wed, 24 Mar 2004 15:13:01 +1100
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
Message-ID: <Sea2-F12rrKJ0gfZe5c0001300f@hotmail.com>


>From: "Dr T. Carver" <tcarver at rfcgr.mrc.ac.uk>
>
>The problem is likely to be that you precompiled emboss before running
>the install script. There is no need, the install script does this for
>you with the correct java flags. Try a 'make clean' and then run the
>install script.

Hi Tim,

I tried make clean and a freshly unpacked source tree but both times when 
executing the install-jemboss-server.sh script with the standalone option 
there is an error in the build phase:

/bin/sh ../../mkinstalldirs /usr/local/emboss/share/EMBOSS/jemboss/lib
/usr/bin/install -c -m 644 README 
/usr/local/emboss/share/EMBOSS/jemboss/lib/README
/usr/bin/install -c -m 644 activation.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/activation.jar
/usr/bin/install -c -m 644 jakarta-regexp-1.2.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar
/usr/bin/install -c -m 644 mail.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/mail.jar
/usr/bin/install -c -m 644 xerces.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/xerces.jar
/usr/bin/install -c -m 644 jalview.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jalview.jar
/usr/bin/install -c -m 644 jcert.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jcert.jar
/usr/bin/install -c -m 644 jnet.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jnet.jar
/usr/bin/install -c -m 644 jsse.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jsse.jar
/usr/bin/install -c -m 644 JembossPrintAlignment.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/JembossPrintAlignment.jar
/usr/bin/install -c -m 644 grout.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/grout.jar
make[4]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
Making install in org
make[2]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
Making install in emboss
make[3]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
Making install in jemboss
make[4]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
Making install in editor
make[5]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make  install-exec-hook
make[7]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/editor
/usr/bin/install: cannot stat `*.class': No such file or directory
make[7]: *** [install-exec-hook] Error 1
make[7]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: *** [install-exec-am] Error 2
make[6]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[5]: *** [install-am] Error 2
make[5]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss'
make: *** [install-recursive] Error 1

--------------------------------------------------------------

EMBASSY packages can optionally be installed along with
the EMBOSS applications, see:
http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/

--------------------------------------------------------------

Install EMBASSY packages (y,n) [y]?
n

-------------------------- ClustalW --------------------------

To use emma (EMBOSS interface to ClustalW) Jemboss needs to
know the path to the clustalw binary.

Enter the path to clustalw or press return to set
this later in jemboss.properties


-------------------------- Primer3  --------------------------

To use eprimer3 (EMBOSS interface primer3 from the Whitehead
Institute) Jemboss needs to know the path to the primer3_core
binary.

Enter the path to primer3_core or press return to set
this later in jemboss.properties

java.io.FileNotFoundException: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/wossname.jar (No such file 
or directory)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
	at sun.tools.jar.Main.run(Main.java:134)
	at sun.tools.jar.Main.main(Main.java:904)
java.io.FileNotFoundException: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/resources.jar (No such file 
or directory)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
	at sun.tools.jar.Main.run(Main.java:134)
	at sun.tools.jar.Main.main(Main.java:904)
error: cannot read: 
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
1 error
error: cannot read: 
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
1 error
mv: cannot stat 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory
touch: creating 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory
./install-jemboss-server.sh: line 362: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 366: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 367: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 370: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 374: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 375: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 381: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 382: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 383: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 384: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 388: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 389: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
cp: cannot stat 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory

Changed /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties
to reflect this installation (original in jemboss.properties.orig)



sed: can't read /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh: No 
such file or directory
mv: cannot stat `/usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh': No 
such file or directory

To run Jemboss:
cd /usr/local/emboss/share/EMBOSS/jemboss
./runJemboss.sh

lt looks like the editor classes are not being built:

$ ls -R -w 80 jemboss/
jemboss/:
editor		  JembossJarUtil.class	JembossParams.java     parser
FileManager.java  JembossJarUtil.java	Jemboss$winExit.class  programs
gui		  Jemboss.java		Makefile	       server
Jemboss$1.class   JembossLogo.java	Makefile.am	       soap
Jemboss.class	  JembossParams.class	Makefile.in

jemboss/editor:
AlignApplet.java			     Makefile
AlignJFrame.java			     Makefile.am
ColourJFrame.java			     Makefile.in
ColourMenu.java				     Matrix.java
ColourPanel.java			     MatrixJFrame.java
Consensus.java				     PatternJFrame.java
ConsensusOptions.java			     PlotConsensus.java
GraphicSequenceCollection.java		     PrettyPlotJFrame.java
GroutAlignJFrameEvent.java		     PrintableJTable.java
GroutAlignJFrame.java			     PrintAlignmentImage.java
GroutAlignJFrameListener.java		     PrintAlignment.java
GroutGraphicSequenceCollectionEvent.java     Sequence.java
GroutGraphicSequenceCollection.java	     SequenceJPanel.java
GroutGraphicSequenceCollectionListener.java  SequenceNameJButton.java
GroutSequence.java			     SequenceProperties.java
GroutSequenceJPanel.java		     SequenceReader.java
IDTableJFrame.java			     SequenceSaver.java

jemboss/gui:
AdvancedOptions$1.class   Makefile			SetUpMenuBar$10.class
AdvancedOptions$2.class   Makefile.am			SetUpMenuBar$11.class
AdvancedOptions.class	  Makefile.in			SetUpMenuBar$1.class
AdvancedOptions.java	  MemoryComboBox.class		SetUpMenuBar$2.class
Browser.java		  MemoryComboBox.java		SetUpMenuBar$3.class
BuildProgramMenu$1.class  ResultsMenuBar.java		SetUpMenuBar$4.class
BuildProgramMenu$2.class  ScrollPanel.class		SetUpMenuBar$5.class
BuildProgramMenu$3.class  ScrollPanel.java		SetUpMenuBar$6.class
BuildProgramMenu$4.class  sequenceChooser		SetUpMenuBar$7.class
BuildProgramMenu$5.class  SequenceData.class		SetUpMenuBar$8.class
BuildProgramMenu$6.class  SequenceData.java		SetUpMenuBar$9.class
BuildProgramMenu$7.class  SequenceList$1.class		SetUpMenuBar.class
BuildProgramMenu$8.class  SequenceList$2.class		SetUpMenuBar.java
BuildProgramMenu.class	  SequenceList$3.class		ShowResultSet.java
BuildProgramMenu.java	  SequenceList$4.class		ShowSavedResults.java
ColumnData.class	  SequenceList$5.class		SplashThread.class
DragJTable.class	  SequenceList$6.class		SplashThread.java
filetree		  SequenceList$7.class		startup
form			  SequenceList.class		SwingWorker.java
ImageIconJPanel.java	  SequenceList.java
LaunchJalView.java	  SequenceListTableModel.class

jemboss/gui/filetree:
DragTree$1.class	      LocalAndRemoteFileTreeFrame$1.class
DragTree$2.class	      LocalAndRemoteFileTreeFrame$2.class
DragTree$3.class	      LocalAndRemoteFileTreeFrame$3.class
DragTree$4.class	      LocalAndRemoteFileTreeFrame$4.class
DragTree$5.class	      LocalAndRemoteFileTreeFrame$5.class
DragTree.class		      LocalAndRemoteFileTreeFrame.class
DragTree.java		      LocalAndRemoteFileTreeFrame.java
DragTree$PopupListener.class  Makefile
FileEditorDisplay.java	      Makefile.am
FileNode$1.class	      Makefile.in
FileNode.class		      RemoteDragTree.java
FileNode.java		      RemoteFileNode.java
FileSave.java		      RemoteFileTreePanel.java
FileSaving.java

jemboss/gui/form:
AlignFormat.java	   Makefile.am		    SetInFileCard.java
ApplicationNamePanel.java  Makefile.in		    SetOutFileCard.java
BuildJembossForm.java	   MultiLineToolTipUI.java  TextFieldFloat.java
JembossComboPopup.java	   PlafMacros.java	    TextFieldInt.java
LabelTextBox.java	   ReportFormat.java	    TextFieldSink.java
ListFilePanel.java	   SectionPanel.java
Makefile		   Separator.java

jemboss/gui/sequenceChooser:
CutNPasteTextArea.java	      Makefile	   OutputSequenceAttributes.java
FileChooser.java	      Makefile.am  SequenceFilter.java
InputSequenceAttributes.java  Makefile.in  TextAreaSink.java

jemboss/gui/startup:
Database.java  Makefile  Makefile.am  Makefile.in  ProgList.java

jemboss/parser:
acd			 AcdVarResolve.java  AjaxUtil.java   Makefile.am
AcdFunResolve.java	 Ajax.class	     Dependent.java  Makefile.in
AcdVariableResolve.java  Ajax.java	     Makefile	     ParseAcd.java

jemboss/parser/acd:
ApplicationFields.java	Makefile     Makefile.in
ApplicationParam.java	Makefile.am

jemboss/programs:
BatchUpdateTimer.java  ResultList.java
JembossProcess.class   ResultsUpdateTimer.java
JembossProcess.java    RunEmbossApplication2.class
ListFile.java	       RunEmbossApplication2.java
Makefile	       RunEmbossApplication2$StderrHandler.class
Makefile.am	       RunEmbossApplication2$StdoutHandler.class
Makefile.in	       RunEmbossApplication.java

jemboss/server:
AppendToLogFileThread.java  JembossServer$3.class  JembossThread.java
JembossAuthServer.java	    JembossServer$4.class  Makefile
JembossFileAuthServer.java  JembossServer$5.class  Makefile.am
JembossFileServer.java	    JembossServer.class    Makefile.in
JembossServer$1.class	    JembossServer.java	   TestPrivateServer.java
JembossServer$2.class	    JembossThread.class    TestPublicServer.java

jemboss/soap:
AuthPopup$1.class  GetACD.java		       PendingResults$2.class
AuthPopup$2.class  GetHelp.java		       PendingResults.class
AuthPopup$3.class  GetWossname.java	       PendingResults.java
AuthPopup$4.class  JembossRun.java	       PrivateRequest.java
AuthPopup$5.class  JembossSoapException.class  PublicRequest.java
AuthPopup$6.class  JembossSoapException.java   ServerSetup$1.class
AuthPopup.class    Makefile		       ServerSetup$2.class
AuthPopup.java	   Makefile.am		       ServerSetup$3.class
CallAjax.java	   Makefile.in		       ServerSetup.class
FileList.java	   MakeFileSafe.java	       ServerSetup.java
FileRoots.java	   PendingResults$1.class      ShowDB.java


Any ideas of what is going wrong?  Is the j2sdk1.3.1 the wrong version to 
use?

Regards

Pierre


--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
Personalise your mobile chart ringtones and polyphonics. Go to  
http://ringtones.com.au/ninemsn/control?page=/ninemsn/main.jsp



From ReduceBodyFat at santagifts01.com  Wed Mar 24 22:45:45 2004
From: ReduceBodyFat at santagifts01.com (Reduce Body Fat)
Date: Thu, 25 Mar 2004 06:45:45 +0300
Subject: [EMBOSS] Lower Blood Pressure and Improve Cholesterol Profile
Message-ID: <idg077Bidgfi1A0ut@santagifts01.com>

An HTML attachment was scrubbed...
URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040325/e75613db/attachment.html 

From pscotney at hotmail.com  Thu Mar 25 02:13:37 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Thu, 25 Mar 2004 18:13:37 +1100
Subject: [EMBOSS] Negotiating a proxy server
Message-ID: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>


Hello,

I have installed EMBOSS-2.8.0 and using the CLI (while I try to get Jemboss 
to work).  I am trying to configure the emboss.defaults file so that I can 
access the EMBL and UNIPROT SRS databases at the www.ebi.ac.uk site.  I have 
read the Administrators guide and I am unsure if I should use SRSWWW or URL 
methods for access.  I have set the entry in emboss.default to:

DB embl [ type: N method: srswww format: embl release: EBI
   dbalias: embl
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "EMBL from EBI"
   ]

DB uniprot [ type: P method: srswww format: swiss release: EBI
   dbalias: uniprot
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "UNIPROT from EBI"
   ]

but then I try

$ seqret -sequence embl:AL627275 -outseq embl_AL627275
Reads and writes (returns) sequences
Error: Unable to read sequence 'embl:AL627275'
Died: seqret terminated: Bad value for '-sequence' and no prompt

This problem is compounded by the fact that I have to access the internet 
via a proxy server which I have SET emboss_proxy "myproxyserver:8080" in the 
emboss.default file.  The problem is the proxy server normally requires a 
username and password (which works for the Galeon browser).  Who can I get 
EMBOSS to issue a username and password to the proxy server for 
authentification?

I apologise for so many questions.

Regards

--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
Personalise your mobile chart ringtones and polyphonics. Go to  
http://ringtones.com.au/ninemsn/control?page=/ninemsn/main.jsp



From pmr at ebi.ac.uk  Thu Mar 25 04:46:11 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 25 Mar 2004 09:46:11 +0000
Subject: [EMBOSS] Negotiating a proxy server
In-Reply-To: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>
References: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>
Message-ID: <4062AA63.6030607@ebi.ac.uk>

Dear Pierre

Pierre Scotney wrote:
> This problem is compounded by the fact that I have to access the 
> internet via a proxy server which I have SET emboss_proxy 
> "myproxyserver:8080" in the emboss.default file.  The problem is the 
> proxy server normally requires a username and password (which works for 
> the Galeon browser).  Who can I get EMBOSS to issue a username and 
> password to the proxy server for authentification?

Sorry, that is not yet in EMBOSS. We do know how to do it, but there has 
been very little demand so it was not implemented. I will try to test it 
and send you an update to try.

regards,

Peter Rice



From areagp61 at yahoo.it  Thu Mar 25 09:17:31 2004
From: areagp61 at yahoo.it (=?iso-8859-1?q?Graziano=20Pappad=E0?=)
Date: Thu, 25 Mar 2004 15:17:31 +0100 (CET)
Subject: [EMBOSS] software to design and execute workflows
Message-ID: <20040325141731.70168.qmail@web21001.mail.yahoo.com>

I would make aware the EMBOSS community about two new
available pieces of software that allow their users to
design and execute complex bioinformatic analysis
processes. They are interesting since these
prototypes, whose names are BioWBI (Bioinformatic
Workflow Builder Interface) and WsBAW (Web services
for Bioinformatic Analysis Workflow) at present wrap a
considerable number (about 40) of EMBOSS algorithms,
besides other algorithms that do not belong to this
package.
These prototypes are made recently available for trial
under alphaworks (http://www.alpaworks.ibm.com).


Regards

Graziano

______________________________________________________________________
Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam
http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/


From areagp61 at yahoo.it  Thu Mar 25 09:54:10 2004
From: areagp61 at yahoo.it (=?iso-8859-1?q?Graziano=20Pappad=E0?=)
Date: Thu, 25 Mar 2004 15:54:10 +0100 (CET)
Subject: [EMBOSS] software to design and execute workflows
Message-ID: <20040325145410.28826.qmail@web21007.mail.yahoo.com>

Hi all,
I have made a mistake in reporting the URL where the
prototypes are available.
The correct link is:
http://www.alphaworks.ibm.com

Regards
Graziano



______________________________________________________________________
Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam
http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/


From gbottu at ben.vub.ac.be  Thu Mar 25 11:59:52 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 25 Mar 2004 17:59:52 +0100
Subject: [EMBOSS] question about databank access methods
Message-ID: <20040325165952.GC24102@bigben.ulb.ac.be>

	Dear colleagues,

I am currently using EMBOSS version 2.8.0. The manual at 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Admin_guide/
adminguide/node4.html#SECTION00421000000000000000
mentions for the databank access method "DIRECT"

DB mydb [ 
#required parameters
   method: "direct"
   format: "embl"
   type: "N"
   dir: "\$emboss_db_dir/mydb"
   file: "*.dat"   
#optional parameters
   fields: "sv des key org"
   release: "63.0"
   comment: "My own database with no indices"
   exclude: "est*.dat"
]

I tried the "exclude" parameter and it did not work. Do I miss something ?
Has someone already used it successfully ?

	Guy Bottu,
	Belgian EMBnet Node


From stefanielager at fastmail.ca  Fri Mar 26 02:45:26 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 26 Mar 2004 07:45:26 +0000 (UTC)
Subject: [EMBOSS] Negotiating a proxy server
Message-ID: <20040326074527.A40F18640CB@mail.interchange.ca>

If it's possible to define domains which you don't want to use proxy for
(as you can do in Mozilla and other web-browsers), that would be nice.
Otherwise you have to use ONLY internal databases or ONLY external
databases, since you often can't go though proxy for internal web pages.

Stefanie

> Dear Pierre
> 
> Pierre Scotney wrote:
>> This problem is compounded by the fact that I have to access the
>> internet via a proxy server which I have SET emboss_proxy
>> "myproxyserver:8080" in the emboss.default file.  The problem is the
>> proxy server normally requires a username and password (which works
>> for the Galeon browser).  Who can I get EMBOSS to issue a username
>> and password to the proxy server for authentification?
> 
> Sorry, that is not yet in EMBOSS. We do know how to do it, but there
> has been very little demand so it was not implemented. I will try to
> test it and send you an update to try.
> 
> regards,
> 
> Peter Rice
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From fnovo at unav.es  Fri Mar 26 04:22:56 2004
From: fnovo at unav.es (F.J. Novo)
Date: Fri, 26 Mar 2004 10:22:56 +0100
Subject: [EMBOSS] refseq IDs via SRSWWW
Message-ID: <4063F670.8020100@unav.es>

Hello, I've just configured a remote access to genbank in my 2.8.0 
installation, as suggested:

DB genbank [ type: N method: srswww format: genbank release: NCBI
    comment: "Genbank from NCBI"
    url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
]

It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems 
unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?
Cheers,


-- 
Dr. Francisco J. Novo
Department of Genetics
University of Navarra
31080 Pamplona (SPAIN)
Tel + 948 425600 (ext 6252)
Fax + 948 425649
www.unav.es/genetica/



From gwilliam at hgmp.mrc.ac.uk  Fri Mar 26 04:27:42 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Fri, 26 Mar 2004 09:27:42 +0000
Subject: [EMBOSS] refseq IDs via SRSWWW
References: <4063F670.8020100@unav.es>
Message-ID: <4063F78E.47946DC9@hgmp.mrc.ac.uk>

RefSeq is a separate database to GenBank.
They are both produced by NCBI.
You will have to retrieve and install these two databases independently.

ftp://ftp.ncbi.nih.gov/genbank
ftp://ftp.ncbi.nih.gov/refseq

Gary Williams

"F.J. Novo" wrote:
> 
> Hello, I've just configured a remote access to genbank in my 2.8.0
> installation, as suggested:
> 
> DB genbank [ type: N method: srswww format: genbank release: NCBI
>     comment: "Genbank from NCBI"
>     url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
> ]
> 
> It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems
> unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?
> Cheers,
> 
> --
> Dr. Francisco J. Novo
> Department of Genetics
> University of Navarra
> 31080 Pamplona (SPAIN)
> Tel + 948 425600 (ext 6252)
> Fax + 948 425649
> www.unav.es/genetica/

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pmr at ebi.ac.uk  Fri Mar 26 04:57:12 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 26 Mar 2004 09:57:12 +0000
Subject: [EMBOSS] refseq IDs via SRSWWW
In-Reply-To: <4063F670.8020100@unav.es>
References: <4063F670.8020100@unav.es>
Message-ID: <4063FE78.1030002@ebi.ac.uk>

F.J. Novo wrote:

> Hello, I've just configured a remote access to genbank in my 2.8.0 
> installation, as suggested:
> 
> DB genbank [ type: N method: srswww format: genbank release: NCBI
>    comment: "Genbank from NCBI"
>    url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
> ]
> 
> It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems 
> unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?

srswww will query by id and acc.

You can query a remote SRS database for any ID or ACC value.

If you define some extra fields, you can query by description, organism 
and keyword.

The NM_xxxxx codes are NCBI's REFSEQ identifiers. GenBank entries may 
refer to them, but they are not indexed by them.

At the Canadian SRS server, the REFSEQ DNA entries are in REFSEQNT so 
you can define that as a database (use dbalias:refseqnt in the EMBOSS db 
definition if you want to use another database name locally)

We have considered providing an Entrez access method to try retrieving 
these strange identifiers (refseq, GI numbers, and so on) from NCBI but 
(a) they change the Entrez interface each time I look and (b) it 
requires far too much rewriting of parsers each time to get to the 
actual entries. Some day, if it becomes stable and if one can query byu 
such fields and get straight to the entries then we may implement it.

Hope this helps,

Peter Rice



From Paul.Baumgartner at unibas.ch  Fri Mar 26 08:48:58 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Fri, 26 Mar 2004 14:48:58 +0100
Subject: [EMBOSS] pdb entries
Message-ID: <54DAE476-7F2C-11D8-8B31-003065B9531E@unibas.ch>

Hi

how should I define the DB pdb [ ? ? ..? ] entry in .embossrc, to 
retrieve coordinates-files from Protein Data Bank (pdb), via 'entret' 
from url: http://srs.ebi.ac.uk/cgi-bin/wgetz ?

Thanks

Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From pseelig at hfriedman.rdsl.lmi.net  Fri Mar 26 22:46:28 2004
From: pseelig at hfriedman.rdsl.lmi.net (doctor)
Date: Sat, 27 Mar 2004 03:46:28 +0000
Subject: [EMBOSS] imemproove your health
In-Reply-To: <H5AAGB69JAD63I7F@embnet.org>
References: <H5AAGB69JAD63I7F@embnet.org>
Message-ID: <7HG99EBB6G6EBCA5@hfriedman.rdsl.lmi.net>

Afteri the age of twenty-onen, your body slowly stopsv releasing an important hormoane known as Human Growgth Hoyrmone. 
The reduction of Human Growpth Hoermone, which regulates levels of other hosrmones in the body (including testosterogne, estrogden, progesterolne, and melatondin) is directly responsible for many of the most common signsn of growing old, such as wrinkles, gray hair, decreased energy, and diminished semxual function. 

Human Growgth Horpmone

Boost your immunen system 
Rejuvenapte your body and mind 
Feel & looka younger 
Reduce wriwnkles, lose weight, decrease cellemulite 
Restore your seex drive and vuigor 
Revitfalize your heart, liver, kidneys & lungs 
Maintain muscloe mass 
Refresh memory, mood and mentaql energy 
Sleep soundldy and awake rested 
Help eliminate stremss, fatigue and depression 2 

Read http://mybestchoice.net/hgh/index.php?pid=eph9058 for more information



From areagp61 at yahoo.it  Fri Mar 26 06:36:44 2004
From: areagp61 at yahoo.it (=?iso-8859-1?Q?Graziano_Pappad=E0?=)
Date: Fri, 26 Mar 2004 12:36:44 +0100
Subject: [EMBOSS] software to design and execute workflows wrong download link
Message-ID: <003d01c41326$a035c560$18105709@JTCDOMAIN>

Hi all,
in the following page http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html#other, it seems that the the BioWBI and WsBAW interfaces can be downloaded at ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz, but this link is wrong!
BioWBI and WsBAW can only be accessed online at the alphaworks site using the following links:

BioWBI       -->     http://www.alphaworks.ibm.com/tech/biowbi
WsBAW     -->     http://www.alphaworks.ibm.com/tech/wsbaw

Regards

Graziano

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From EliminateBugs at bargainsdaily01.com  Sun Mar 28 22:34:30 2004
From: EliminateBugs at bargainsdaily01.com (Eliminate Bugs)
Date: Mon, 29 Mar 2004 07:34:30 +0400
Subject: [EMBOSS] Complimentary Scan for your PC
Message-ID: <idg077Bidgfi1A0ut@bargainsdaily01.com>

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URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040329/1046b794/attachment.html 

From letondal at pasteur.fr  Mon Mar 29 03:24:44 2004
From: letondal at pasteur.fr (Catherine Letondal)
Date: Mon, 29 Mar 2004 10:24:44 +0200
Subject: [EMBOSS] software to design and execute workflows wrong download link 
In-Reply-To: Your message of "Fri, 26 Mar 2004 12:36:44 +0100."
             <003d01c41326$a035c560$18105709@JTCDOMAIN> 
Message-ID: <200403290824.i2T8Oibc452617@electre.pasteur.fr>


Graziano_Pappad? wrote:
> 
> Hi all,
> in the following page =
> http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html#other, it =
> seems that the the BioWBI and WsBAW interfaces can be downloaded at =
> ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz, but this =
> link is wrong!

It's not. I have just checked it. 
(we had some Internet connection problems these days, thank you Worldcom)

> BioWBI and WsBAW can only be accessed online at the alphaworks site =
> using the following links:
> 
> BioWBI       -->     http://www.alphaworks.ibm.com/tech/biowbi
> WsBAW     -->     http://www.alphaworks.ibm.com/tech/wsbaw
> 
> Regards
> 
> Graziano
> 
> 
>

--
Catherine Letondal -- Pasteur Institute Computing Center


From ranrub at md.huji.ac.il  Mon Mar 29 10:02:12 2004
From: ranrub at md.huji.ac.il (Ran Rubinstein)
Date: Mon, 29 Mar 2004 17:02:12 +0200
Subject: [EMBOSS] Negotiating a proxy server
In-Reply-To: <20040326074527.A40F18640CB@mail.interchange.ca>
Message-ID: <006b01c4159e$d11c5ed0$7ea74084@sauron>

Pierre,

It's possible to circumvent the proxy password problem by installing a local
squid proxy on your machine (or any other machine) and having it access the
password protected proxy as a parent proxy (squid supports password
authentication).
In your emboss.default you then define the proxy as localhost:3128 or
however you installed squid.

Hope this helps,
--?
Ran Rubinstein 
Dept. of Molecular Biology 
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992


-----Original Message-----
From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On
Behalf Of Stefanie Lager
Sent: Friday, March 26, 2004 9:45 AM
To: emboss at embnet.org
Subject: Re: [EMBOSS] Negotiating a proxy server

If it's possible to define domains which you don't want to use proxy for
(as you can do in Mozilla and other web-browsers), that would be nice.
Otherwise you have to use ONLY internal databases or ONLY external
databases, since you often can't go though proxy for internal web pages.

Stefanie

> Dear Pierre
> 
> Pierre Scotney wrote:
>> This problem is compounded by the fact that I have to access the
>> internet via a proxy server which I have SET emboss_proxy
>> "myproxyserver:8080" in the emboss.default file.  The problem is the
>> proxy server normally requires a username and password (which works
>> for the Galeon browser).  Who can I get EMBOSS to issue a username
>> and password to the proxy server for authentification?
> 
> Sorry, that is not yet in EMBOSS. We do know how to do it, but there
> has been very little demand so it was not implemented. I will try to
> test it and send you an update to try.
> 
> regards,
> 
> Peter Rice
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



From jison at hgmp.mrc.ac.uk  Mon Mar 29 14:08:00 2004
From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison)
Date: Mon, 29 Mar 2004 20:08:00 +0100
Subject: [EMBOSS] pdb entries
References: <54DAE476-7F2C-11D8-8B31-003065B9531E@unibas.ch>
Message-ID: <40687410.57D9C187@hgmp.mrc.ac.uk>

Hi Paul

PDB is not (yet) fully supported under EMBOSS.

There are functions to parse PDB files and applications
to do the same and generate "clean" files of coordinate
and derived data, but PDB format is not (yet) suported
in the way I think you envisage using it.

Let me know what you want to do with PDB and why and
I'll see if EMBOSS can (be made to) do it.

Cheers

Jon


Paul Baumgartner wrote:

> Hi
>
> how should I define the DB pdb [ ? ? ..? ] entry in .embossrc, to
> retrieve coordinates-files from Protein Data Bank (pdb), via 'entret'
> from url: http://srs.ebi.ac.uk/cgi-bin/wgetz ?
>
> Thanks
>
> Biozentrum
> Paul Baumgartner
> Zellbiologie
> Klingelbergstrasse 70
> CH-4056 Basel

--
Jon C. Ison, PhD
Proteomics Applications Group
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: jison at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk






From kayttotuki at vtt.fi  Mon Mar  1 12:55:06 2004
From: kayttotuki at vtt.fi (kayttotuki at vtt.fi)
Date: Mon, 1 Mar 2004 14:55:06 +0200 (EET)
Subject: [EMBOSS] [#ID:71296#] Re: Document
In-Reply-To: <200403011253.i21CrM4v002570@mailgw.vtt.fi>
Message-ID: <4147547.1078145705781.JavaMail.SYSTEM@espsr05>

Kiitos. Viestisi on tallennettu ty?nhallintaj?rjestelm??mme.


From heltondz at artnet.com.br  Mon Mar  1 16:45:47 2004
From: heltondz at artnet.com.br (Ollie J. Helton)
Date: Mon, 01 Mar 2004 16:45:47 +0000
Subject: [EMBOSS] =?iso-8859-1?B?Q29zdGluZyB0byBtdWNoIGZvciB5b3UgUHJlc2NyaXAldGlvbiBEcil1Z3M/Pz8gQ2hlY2sgdGhpcyBvdXQh?=
Message-ID: <dba301c3ffac$cf31e8cc$39b5def1@8m4fph2>



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From BugEliminator at online-bargains01.com  Tue Mar  2 04:38:48 2004
From: BugEliminator at online-bargains01.com (Bug Eliminator)
Date: Tue, 02 Mar 2004 07:38:48 +0300
Subject: [EMBOSS] Complimentary Scan for your PC
Message-ID: <idg077Bidgfi1A0ut@online-bargains01.com>

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From didactic at itb.cnr.it  Tue Mar  2 15:17:34 2004
From: didactic at itb.cnr.it (didactic at itb.cnr.it)
Date: Tue, 02 Mar 2004 16:17:34 +0100
Subject: [EMBOSS] ello! =))
Message-ID: <suhvqdbshaaxdjttdkl@itb.cnr.it>

Looking forward for a response :P

68026  --  archive password
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From NAIILRIILRIKENX at ILRI.EXCH.CGIAR.ORG  Tue Mar  2 15:32:10 2004
From: NAIILRIILRIKENX at ILRI.EXCH.CGIAR.ORG (GroupShield for Exchange (ILRIKENX))
Date: Tue, 02 Mar 2004 07:32:10 -0800
Subject: [EMBOSS] ALERT -  GroupShield ticket number OA0_1078241530_ILRIKENX_1 was
	generated
Message-ID: <1F95CCD444D8D21180250090273F21FD069FC1AF@ILRIKENX>

Action Taken:
The attachment was deleted from the message and replaced with a text file
informing the recipient of the action taken.

To:
emboss at embnet.org <emboss at embnet.org>

From:
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[EMBOSS] ello! =))

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From support at embnet.org  Wed Mar  3 08:38:32 2004
From: support at embnet.org (support at embnet.org)
Date: Wed, 03 Mar 2004 18:38:32 +1000
Subject: [EMBOSS] E-mail account security warning.
Message-ID: <sdcryfrmevmjttrxdoy@embnet.org>

Dear user of Embnet.org gateway e-mail server,

Your e-mail  account has been temporary disabled because of  unauthorized access.

For  further details see  the attach.

Attached file protected with  the password for security  reasons. Password  is 11463.

The Management,
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From siegmund at develogen.com  Thu Mar  4 10:42:34 2004
From: siegmund at develogen.com (Thomas Siegmund)
Date: Thu, 4 Mar 2004 11:42:34 +0100
Subject: [EMBOSS] Kaptain user interface, new release
Message-ID: <200403041142.34847.siegmund@develogen.com>

*This message was transferred with a trial version of CommuniGate(tm) Pro*
Hi everybody,

there is a new release of the EMBOSS.kaptn graphical user interface for EMBOSS 
running on Linux/X11 or MacOSX. Version 0.96 of the GUI is basically a bugfix 
release for use with EMBOSS 2.8.0.

Due to considerable efforts of the EMBOSS programmers towards a more 
consistent command line interface many emboss qualifiers have been changed or 
renamed during the last few EMBOSS releases. Unfortunately many of these 
changes were not listed in the EMBOSS ChangeLog. Therefore EMBOSS and the GUI 
have drifted apart to an unacceptable degree.

In order to fix this I made a little script to check the kaptain grammars 
against the acd files of a given EMBOSS release. I now have fixed all the 
problems shown by the script running against EMBOSS 2.8.0 . I'd recommend 
everybody using the Kaptain GUI with EMBOSS 2.8.0 to get the 0.96 version of 
the GUI. As you can see from the ChangeLog there were quite a few fixes to 
do :-0

Download, as usual, from 

http://userpage.fu-berlin.de/~sgmd/download.html

From the ChangeLog:

Version 0.96 - Use with EMBOSS 2.8
----------------------------------------------
- -startbase, -endbase, -separate for abiview.kaptn
- -aadata  for charge.kaptn
- -addlast , -report -> -outfile for checktrans.kaptn
- -sum for chips.kaptn
- -seqout -> -outseq in coderet.kaptn
- -obsexp, -cg, -pc and a new layout for cpgplot.kaptain
- small fix for cutgextract
- -aadata for digest.kaptn
- -maxrepeat for einverted
- -full for embossversion
- -nhydrophylic -> nohgap in emma.kaptn
- -onlydend for emma.kaptn
- -sequences -> -sequence in emowse.kaptn
- -aadata for emowse.kaptn
- removed -mmshow- -raccshow, and  -rdescshow from fuzznuc.kaptn,
  fuzzpro.kaptn, fuzztran.kaptn
- maxsize for getorf.kaptn
- -gi, -version for infoseq.kaptn
- -interticks for lindna.kapnt
- -outlist -> -outfile in listor.kaptn
- -report -> outfile in megamerger.kaptn
- -other -> -othersequence in merger.kaptn
- -showdel for mwfilter.kaptn
- -brief for needle.kaptn
- -sequencea -> -sequence in octanol.kaptn
- -insequence -> -sequence in palindrome.kaptn
- -sequence,-insseq -> -[ab]sequence
   and a cleaner layout for pasteseq.kaptn
- -insseq -> -sequence for pepinfo.kaptn
- -aadata for pepstats.kaptn
- -wheel for pepwheel.kaptn
- -msf -> -sequences for pepwindowall.kaptn
- -msf -> -sequences, remove -nodata in plotcon.kaptn
- -start, -stop for plotorf.kaptn
- -msf -> -sequences for prettyplot.kaptn
- -sequence -> -seqall for primersearch.kaptn
- added -name, -description, removed -preferred from remap.kaptn
- added -blunt, -sticky, removed -preferred from remap.kaptn
- added -datafile, removed -preferred from restrict.kaptn
- -feature for seqret.kaptn
- -strittags for showfeat.kaptn
- remove -preferred from showseq.kaptn
- -primers -> -primersfile, -sequences -> -seqall in stssearch.kaptn
- -msf -> -sequences in tmap.kaptn
- -nseq -> -asequence, -pseq -> -bsequence in tranalign.kaptn
- -feature for skipseq.kaptn
- -gapextend, -gapopen for supermatcher.kaptn
- -casesensitive for textsearch.kaptn (doesn't seem to work)
- -minlength, -custom for tfscan.kaptn
- -brief for water.kaptn
- added kaptncheck.pl, a quick hack to compare kaptain grammars
  with the acd files of a given EMBOSS release
- added sixpack.kaptn

Version 0.95 "Bangkok edition"
- remove -data in pepwheel.kapnt, pepnet.kaptn
- make -msf -sequence in all ephylip programms
- small fixes in needle.kaptn, water.kaptn

Version 0.94
- renamed pestfind.kaptn to epestfind.kaptn
- sequencea -> sequence in pepstats.kaptn
- rformat option for dreg.kaptn, preg.kaptn, recoder.kaptn, silent.kaptn

Regards,

Thomas

-- 
Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

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From acorbe2 at emory.edu  Thu Mar  4 16:03:12 2004
From: acorbe2 at emory.edu (Anita Corbett)
Date: Thu, 4 Mar 2004 11:03:12 -0500 (EST)
Subject: [EMBOSS] Out of Office
Message-ID: <200403041603.i24G3CKG002824@euphrosyne.cc.emory.edu>

I am out of the office until March 8, 2004.
Although I may have some e-mail access, it is likely that your mail regarding "Your bill." will be read when I return.
If you have something urgent, please contact someone in my lab (4158 RRC) at 404-727-4504.  Start with either Michelle (mtharre at emory.edu) or Sara (sleung at emory.edu).


From Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl  Fri Mar  5 11:19:20 2004
From: Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl (Symantec_AntiVirus_for_SMTP_Gateways at lumc.nl)
Date: Fri, 05 Mar 2004 12:19:20 +0100
Subject: [EMBOSS] LUMC detected a problem with an email that appears to be received from you.
Message-ID: <20040305111921.4F73A7D0C9@mercury.hgmp.mrc.ac.uk>

The LUMC does not allow our users to receive
certain types of email.

In case of attachment blocking:
Your email is delivered to the recipient,
but attachment(s) have been removed.
Please place them in a ZIP file or send an URL to
the recipient to make them available for download.

In case of subject blocking:
Please rephrase your subject line.
Your email has NOT reached the intended recipient.

Please note that if you did not send a message to our recipient,
a number of computer viruses make it appear that the
author of a message is someone else.
If that's happened to you and you did not send the message
referred to below, please disregard this message.

From: emboss at embnet.org
To: j.a.maassen at lumc.nl

Subject: hello

Matching Subject: hello




From yann-francois.bizouerne at bayercropscience.com  Fri Mar  5 15:32:40 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Fri, 5 Mar 2004 16:32:40 +0100
Subject: [EMBOSS] question about "recoder" tool
Message-ID: <OFAC25D872.092BC3E7-ONC1256E4E.00551028-C1256E4E.00556389@bayer.de>





Hi,

I have the Emboss version  2.7.1 installed on our servers.
I try to execute the "recoder" tool as below.

   > recoder
   Remove restriction sites but maintain the same translation
   Nucleic acid sequence: seq.test
   Comma separated enzyme list [all]:
   Results file name [aa749534.recoder]:

      EMBOSS An error in recoder.c at line 380:
   Aborting...restriction file not found


It seems to not found the restriction file. Where can I get one ? And where put
it in Emboss directory ?

Thanks in advance


Yann-Fran?ois BIZOUERNE
BioInformatic Team
BAYER CropScience
4, rue Pierre Fontaine
91058 Evry Cedex
FRANCE
Phone:      33-(0) 1-69-47-61-56
FAX:        33-(0) 1-69-47-61-42
E-mail:     yann-francois.bizouerne at bayercropscience.com
Intranet: http://bioinfo.evry.fr.bayercropscience/



From gwilliam at hgmp.mrc.ac.uk  Fri Mar  5 15:39:31 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Fri, 05 Mar 2004 15:39:31 +0000
Subject: [EMBOSS] question about "recoder" tool
References: <OFAC25D872.092BC3E7-ONC1256E4E.00551028-C1256E4E.00556389@bayer.de>
Message-ID: <40489F33.6F2497BD@hgmp.mrc.ac.uk>


   This uses the EMBOSS REBASE data files in 'data/REBASE/*' under the
   EMBOSS installation directory.

   These files must first be set up using the program 'rebaseextract'.
   Running 'rebaseextract' may be the job of your system manager.

   See the documentation of rebaseextract for more details:
   http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/rebaseextract.html

Gary


yann-francois.bizouerne at bayercropscience.com wrote:
> 
> Hi,
> 
> I have the Emboss version  2.7.1 installed on our servers.
> I try to execute the "recoder" tool as below.
> 
>    > recoder
>    Remove restriction sites but maintain the same translation
>    Nucleic acid sequence: seq.test
>    Comma separated enzyme list [all]:
>    Results file name [aa749534.recoder]:
> 
>       EMBOSS An error in recoder.c at line 380:
>    Aborting...restriction file not found
> 
> It seems to not found the restriction file. Where can I get one ? And where put
> it in Emboss directory ?
> 
> Thanks in advance
> 
> Yann-Fran?ois BIZOUERNE
> BioInformatic Team
> BAYER CropScience
> 4, rue Pierre Fontaine
> 91058 Evry Cedex
> FRANCE
> Phone:      33-(0) 1-69-47-61-56
> FAX:        33-(0) 1-69-47-61-42
> E-mail:     yann-francois.bizouerne at bayercropscience.com
> Intranet: http://bioinfo.evry.fr.bayercropscience/

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From tchiang at bioinfo.sickkids.on.ca  Fri Mar  5 18:36:52 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Fri, 5 Mar 2004 13:36:52 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
Message-ID: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>


Hi,

I ran dbiflat on a swissprot flatfile with the option '-fields taxon' in
order to index the db by species.  All went well, and there were files:

taxon.hit
taxon.trg

produced in addition to the division.lkp and entrynam.idx.

My question is how do I now retrieve only the records that are for a given
species, ie.

$ entret swtest:HOMO
Reads and writes (returns) flatfiles entries
Error: Database Entry 'HOMO' not found
Error: Unable to read sequence 'swtest:HOMO'



I know the dbiflat worked, because when I run

$ entret swtest:*

I get all the files in the database.


Thanks for the help.



-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================




From jlaroche at bioinfo.ulaval.ca  Fri Mar  5 18:47:18 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Fri, 5 Mar 2004 13:47:18 -0500
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>
References: <Pine.GSO.4.05.10403051330070.22835-100000@kenny.bioinfo.sickkids.on.ca>
Message-ID: <8748F918-6ED5-11D8-8A37-000A95CDA6C0@bioinfo.ulaval.ca>

Try this:

entret swtest-taxon:homo

If you want to use wildcard, you type :

entret swtest-taxon:homo\*


J?r?me

Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca
Le 04-03-05, ? 13:36, Ted Chiang a ?crit :

>
> Hi,
>
> I ran dbiflat on a swissprot flatfile with the option '-fields taxon' 
> in
> order to index the db by species.  All went well, and there were files:
>
> taxon.hit
> taxon.trg
>
> produced in addition to the division.lkp and entrynam.idx.
>
> My question is how do I now retrieve only the records that are for a 
> given
> species, ie.
>
> $ entret swtest:HOMO
> Reads and writes (returns) flatfiles entries
> Error: Database Entry 'HOMO' not found
> Error: Unable to read sequence 'swtest:HOMO'
>
>
>
> I know the dbiflat worked, because when I run
>
> $ entret swtest:*
>
> I get all the files in the database.
>
>
> Thanks for the help.
>
>
>
> -Ted
>
>
> =====================================
> Ted Chiang, Analyst
> Centre for Computational Biology
> Hospital for Sick Children, Toronto
> 416.813.7028
> tchiang at bioinfo.sickkids.on.ca
> =====================================
>



From tchiang at bioinfo.sickkids.on.ca  Fri Mar  5 20:54:46 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Fri, 5 Mar 2004 15:54:46 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <8748F918-6ED5-11D8-8A37-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>


Thanks, but that doesn't seem to work.  Here is a record of what I did.


$dbiflat -fields=taxon
Index a flat file database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]:
Database directory [.]:
Wildcard database filename [*.dat]: *.test
Database name: swtest
Release number [0.0]:
Index date [00/00/00]:


$ls -l
-rw-r--r--           322 Mar  5 15:46 division.lkp
-rw-r--r--         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--       2081272 Mar  5 12:27 sw.test
-rw-r--r--         29176 Mar  5 15:46 taxon.hit
-rw-r--r--         64411 Mar  5 15:46 taxon.trg


$showdb -database swtest
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
swtest        P    OK  OK  OK  Swissprot indexed by field <taxon>


$entret swtest-taxon:homo\*
Reads and writes (returns) flatfile entries
Error: USA 'swtest-taxon:homo*' query field 'taxon' not defined for
database 'swtest'
Error: Unable to read sequence 'swtest-taxon:homo*'


$entret swtest:*
Reads and writes (returns) flatfile entries
Output file [hs11_arath.entret]: all_entries

$ls -l
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 15:51 all_entries
-rw-r--r--    1 tchiang  jamie           322 Mar  5 15:46 division.lkp
-rw-r--r--    1 tchiang  jamie         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 12:27 sw.test
-rw-r--r--    1 tchiang  jamie         29176 Mar  5 15:46 taxon.hit
-rw-r--r--    1 tchiang  jamie         64411 Mar  5 15:46 taxon.trg


----------------------------------------------


-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Fri, 5 Mar 2004, [ISO-8859-1] J?r?me Laroche wrote:

> Try this:
> 
> entret swtest-taxon:homo
> 
> If you want to use wildcard, you type :
> 
> entret swtest-taxon:homo\*
> 
> 
> J?r?me
> 
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> Le 04-03-05, ? 13:36, Ted Chiang a ?crit :
> 
> >
> > Hi,
> >
> > I ran dbiflat on a swissprot flatfile with the option '-fields taxon' 
> > in
> > order to index the db by species.  All went well, and there were files:
> >
> > taxon.hit
> > taxon.trg
> >
> > produced in addition to the division.lkp and entrynam.idx.
> >
> > My question is how do I now retrieve only the records that are for a 
> > given
> > species, ie.
> >
> > $ entret swtest:HOMO
> > Reads and writes (returns) flatfiles entries
> > Error: Database Entry 'HOMO' not found
> > Error: Unable to read sequence 'swtest:HOMO'
> >
> >
> >
> > I know the dbiflat worked, because when I run
> >
> > $ entret swtest:*
> >
> > I get all the files in the database.
> >
> >
> > Thanks for the help.
> >
> >
> >
> > -Ted
> >
> >
> > =====================================
> > Ted Chiang, Analyst
> > Centre for Computational Biology
> > Hospital for Sick Children, Toronto
> > 416.813.7028
> > tchiang at bioinfo.sickkids.on.ca
> > =====================================
> >
> 
> 



From jlaroche at bioinfo.ulaval.ca  Sat Mar  6 19:49:03 2004
From: jlaroche at bioinfo.ulaval.ca (=?ISO-8859-1?Q?J=E9r=F4me_Laroche?=)
Date: Sat, 6 Mar 2004 14:49:03 -0500
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>
References: <Pine.GSO.4.05.10403051540270.24541-100000@kenny.bioinfo.sickkids.on.ca>
Message-ID: <52550CFD-6FA7-11D8-8A9B-000A95CDA6C0@bioinfo.ulaval.ca>

Hi Ted,

Try this:

1. dbiflat -fields taxon
choose the right format of your flatfile: entry format

2. Add the following lines in your .embossrc file:

DB swtest [
    type: N
    method: emblcd
    format: genbank <-specify the format
    dir: path    <- the path of your database
    indexdir: path   <-the path of your index files
    fields: org		<-the field you have indexed
]
3. seqret swtest-org:homo

I run a couple of test and it works. But you should knwo that not all 
words in the field  ORGANISM are indexed. Just those of taxonomic 
significance.

So in a genbank flatfile containing the following organism field for 
two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
viruses, no RNA stage' use together or alone were not recognized even 
if they are in the organism field.

   ORGANISM  Agrobacterium sp.
             Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
             Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
  or

   ORGANISM  Chlorella virus
             Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
Chlorovirus.



Good luck!


J?r?me
Centre de bioinformatique
Pavillon Charles-Eug?ne-Marchand
Bureau 4233d
t?l: 418-656-2131 poste 6184
fax: 418-656-7176
www.bioinfo.ulaval.ca


From yann-francois.bizouerne at bayercropscience.com  Mon Mar  8 07:28:54 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Mon, 8 Mar 2004 08:28:54 +0100
Subject: [EMBOSS] Need more info about REBASEEXTRACT
Message-ID: <OF09522F50.64983652-ONC1256E51.00281C58-C1256E51.0029195C@bayer.de>





Hello,

I try to use REBASEEXTRACT and I have the following error message

   > rebaseextract
   Extract data from REBASE
   Full pathname of WITHREFM file:
   /tools/bioinfo/app/Emboss/share/EMBOSS/data/REBASE/withrefm
   Full pathname of PROTO file:
   /tools/bioinfo/app/Emboss/share/EMBOSS/data/REBASE/proto

      EMBOSS An error in rebaseextract.c at line 161:
   Invalid withrefm file

I just donwload the last version of the withrefm and proto files from REBASE ftp
site (withrefm.403 & proto.403). I have rename these files as withrefm & proto
I have put these files in the path you can see above and I have run the
REBASEEXTRACT command.
Did I miss something ?



Yann BIZOUERNE




From yann-francois.bizouerne at bayercropscience.com  Mon Mar  8 08:30:58 2004
From: yann-francois.bizouerne at bayercropscience.com (yann-francois.bizouerne at bayercropscience.com)
Date: Mon, 8 Mar 2004 09:30:58 +0100
Subject: [EMBOSS] Please forget my precedent mail about REBASEEXTRACT. I found the solution
Message-ID: <OFB38A5D05.A509D0BC-ONC1256E51.002E99DD-C1256E51.002EC7E8@bayer.de>





I soluce my problem.
Sorry for the disturbance.



Yann BIZOUERNE



From isabelle.wells at Roche.COM  Mon Mar  8 09:06:04 2004
From: isabelle.wells at Roche.COM (Wells, Isabelle {PRBI~Basel})
Date: Mon, 08 Mar 2004 10:06:04 +0100
Subject: [EMBOSS] Problem with indexing of large files and seqret
Message-ID: <062896243F02D445AB77BD2B51E2F3730258AF@rbamsem3.emea.roche.com>

Hello all,

We have installed the emboss package 2.8.0 on both IRIX and Linux (64
bit) machines.  I have installed several databases, one of which is the
incremental updates of EMBL which we cumulate in a flat file now larger
than 2 GB. This database was successfully indexed using dbiflat, but we
have the problem that seqret either is enable to read a sequence and
dies or goes to a segmentation fault, depending on the position of the
sequence to read. 

I saw in the mailing list archives that this problem was already
mentioned in 2002, but is there now a way to solve it without splitting
the large flat file?

Thanks for your help,
Isabelle Wells

+--- O---O -------------------------------------------
      o-o         Isabelle Wells, Ph. D.
       O          Bioinformatics group
      o-o         F. Hoffmann-La Roche Ltd  
     o---o        PRBI-B, building 65/307
    o----o        CH-4070 Basel, Switzerland
   O----O         
   0--o           
     O	       
    o-o           E-mail: isabelle.wells at roche.com   
+- o---o ---------------------------------------------


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From David.Bauer at SCHERING.DE  Mon Mar  8 13:33:05 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Mon, 8 Mar 2004 14:33:05 +0100
Subject: [EMBOSS] staden gui
Message-ID: <OF5971F6E7.20C380B9-ONC1256E51.0049E191@schering.de>

Hello,

I have some problems getting the staden package installed.
All parts which do not use the iwidgets stuff are OK (gap4, trev).
But with spin, pregap4 etc. I'm getting the error messages below.
Any hints why the itcl3.3/itk3.3 part is not working ?

Thanks,
David.

> spin
unknown namespace in import pattern "itcl::*"
    while executing
"namespace import itcl::*"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/iwidgetsrc"
 line 12)
    invoked from within
"source
/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/iwidgetsrc"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list source $i]"
    (procedure "SetDefaults" line 42)
    invoked from within
"SetDefaults $tdir ${name}rc ${name}_defs"
    (procedure "simple_load_package" line 36)
    invoked from within
"simple_load_package $tcldir"
    (procedure "load_package" line 5)
    invoked from within
"load_package iwidgets"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/spinrc"
 line 8)
    invoked from within
"source
/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../tables/spinrc"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list source $i]"
    (procedure "SetDefaults" line 42)
    invoked from within
"SetDefaults $tdir ${name}rc ${name}_defs"
    (procedure "simple_load_package" line 36)
    invoked from within
"simple_load_package $tcldir"
    (procedure "load_package" line 5)
    invoked from within
"load_package spin"
    (file
"/usr/home/sg46237/Biosoft/Staden/staden-src-rel-1-4/linux-bin/../lib/spin/spin.tcl"
 line 270)




From tchiang at bioinfo.sickkids.on.ca  Mon Mar  8 15:34:47 2004
From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang)
Date: Mon, 8 Mar 2004 10:34:47 -0500 (EST)
Subject: [EMBOSS] dbiflat and entret...
In-Reply-To: <52550CFD-6FA7-11D8-8A9B-000A95CDA6C0@bioinfo.ulaval.ca>
Message-ID: <Pine.GSO.4.05.10403081033590.9111-100000@kenny.bioinfo.sickkids.on.ca>

Jerome,

Thanks for your help.  Things seems to work pretty good.

-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Sat, 6 Mar 2004, [ISO-8859-1] J?r?me Laroche wrote:

> Hi Ted,
> 
> Try this:
> 
> 1. dbiflat -fields taxon
> choose the right format of your flatfile: entry format
> 
> 2. Add the following lines in your .embossrc file:
> 
> DB swtest [
>     type: N
>     method: emblcd
>     format: genbank <-specify the format
>     dir: path    <- the path of your database
>     indexdir: path   <-the path of your index files
>     fields: org		<-the field you have indexed
> ]
> 3. seqret swtest-org:homo
> 
> I run a couple of test and it works. But you should knwo that not all 
> words in the field  ORGANISM are indexed. Just those of taxonomic 
> significance.
> 
> So in a genbank flatfile containing the following organism field for 
> two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
> viruses, no RNA stage' use together or alone were not recognized even 
> if they are in the organism field.
> 
>    ORGANISM  Agrobacterium sp.
>              Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
>              Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
>   or
> 
>    ORGANISM  Chlorella virus
>              Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
> Chlorovirus.
> 
> 
> 
> Good luck!
> 
> 
> J?r?me
> Centre de bioinformatique
> Pavillon Charles-Eug?ne-Marchand
> Bureau 4233d
> t?l: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> 



From louis at gtptech.com  Tue Mar  9 15:05:31 2004
From: louis at gtptech.com (Carole Louis)
Date: 09 Mar 2004 16:05:31 +0100
Subject: [EMBOSS] CUTG
Message-ID: <1078844731.3235.6.camel@Coriandre>

Hi,

I extracted the CUTG database with cutgextract without any problem but
I'd like to have a more explicite name for my .cut files ? Is it
possible to obtain it ?

Thanks,

-- 
Carole Louis <louis at gtptech.com>
GTP Technology
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From areagp61 at yahoo.it  Tue Mar  9 15:17:23 2004
From: areagp61 at yahoo.it (Graziano P.)
Date: Tue, 9 Mar 2004 16:17:23 +0100
Subject: [EMBOSS] CUTG
References: <1078844731.3235.6.camel@Coriandre>
Message-ID: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>

Hi Carol,
not every file but most are described in the README file from ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list I am using.

Regards
Graziano

Easn.cut  -  Aspergillus nidulans
Eath.cut  -  Arabidopsis thaliana
Ebly.cut  -  Hordeum vulgare (Barley)
Ebmo.cut  -  Bombyx mori (Silk Moth)
Ebov.cut  -  Bos taurus (Cow)
Ebsu.cut  -  Bacillus subtilis
Ecel.cut  -  Caenorhabditis elegans
Echi.cut  -  Chironomus sp.
Echk.cut  -  Gallus sp. (Chicken)
Eddi.cut  -  Dictyostelium discoideum
Edro.cut  -  Drosophila melanogaster
Eeco.cut  -  Escherichia coli
Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
Ehum.cut  -  Homo sapiens
Ekpn.cut  -  Klebsiella pneumoniae
Emac.cut  -  Macaca sp
Emus.cut  -  Mus sp. (Mouse)
Emze.cut  -  Zea mays (Maize)
Emzecp.cut  -  Zea mays chloroplast (Maize)
Eneu.cut  -  Neurospora crassa
Engo.cut  -  Neisseria gonorrheae
Epea.cut  -  Pisum sativum (Pea)
Epet.cut  -  Petunia sp.
Epfa.cut  -  Plasmodium falciparum
Ephv.cut  -  Phaseolus vulgaris (Lima bean)
Epot.cut  -  Solanum tuberosum (Pototoe)
Epse.cut  -  Pseudomonas sp.
Erab.cut  -  Oryctolagus sp. (Rabbit)
Erat.cut  -  Rattus sp. (Rat)
Erhm.cut  -  Rhizobium meliloti
Eric.cut  -  Oryza sativa (Rice)
Eshp.cut  -  Ovis sp. (Sheep)
Eslm.cut  -  Physarum polycephalum
Esoy.cut  -  Glycine max (Soybean)
Esta.cut  -  Staphylococcus aureus
Esty.cut  -  Salmonella thphimurium
Esus.cut  -  Strongylocentrotus purpuratus
Etob.cut  -  Nicotiana tabacum (Tobacco)
Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
Etom.cut  -  Lycopersicon esculentum (Tomato)
Etrb.cut  -  Trypanosoma brucei
Ewht.cut  -  Triticum aestivum (Wheat)
Exel.cut  -  Xenopus laevis
Eysc.cut  -  Saccharomyces cerevisiae
Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
Eysp.cut  -  Schizosaccharomyces pombe


----- Original Message ----- 
  From: Carole Louis 
  To: Liste Emboss 
  Sent: Tuesday, March 09, 2004 4:05 PM
  Subject: [EMBOSS] CUTG


  Hi,

  I extracted the CUTG database with cutgextract without any problem but I'd like to have a more explicite name for my .cut files ? Is it possible to obtain it ?

  Thanks,

        -- 
        Carole Louis <louis at gtptech.com>
        GTP Technology  
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From louis at gtptech.com  Wed Mar 10 08:31:23 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 09:31:23 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
Message-ID: <1078907483.3235.21.camel@Coriandre>

Thank you. I'm looking for Spodoptera frugiperda. I thought it was
Espo.cut but it seems very different of the table I found at
http://www.kazusa.or.jp/codon/. 


Le mar 09/03/2004 ? 16:17, Graziano P. a ?crit :

> ? 
> Hi Carol,
> not every file but most are described in the README file from
> ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list
> I am using.
>  
> Regards
> Graziano
>  
> Easn.cut  -  Aspergillus nidulans
> Eath.cut  -  Arabidopsis thaliana
> Ebly.cut  -  Hordeum vulgare (Barley)
> Ebmo.cut  -  Bombyx mori (Silk Moth)
> Ebov.cut  -  Bos taurus (Cow)
> Ebsu.cut  -  Bacillus subtilis
> Ecel.cut  -  Caenorhabditis elegans
> Echi.cut  -  Chironomus sp.
> Echk.cut  -  Gallus sp. (Chicken)
> Eddi.cut  -  Dictyostelium discoideum
> Edro.cut  -  Drosophila melanogaster
> Eeco.cut  -  Escherichia coli
> Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
> Ehum.cut  -  Homo sapiens
> Ekpn.cut  -  Klebsiella pneumoniae
> Emac.cut  -  Macaca sp
> Emus.cut  -  Mus sp. (Mouse)
> Emze.cut  -  Zea mays (Maize)
> Emzecp.cut  -  Zea mays chloroplast (Maize)
> Eneu.cut  -  Neurospora crassa
> Engo.cut  -  Neisseria gonorrheae
> Epea.cut  -  Pisum sativum (Pea)
> Epet.cut  -  Petunia sp.
> Epfa.cut  -  Plasmodium falciparum
> Ephv.cut  -  Phaseolus vulgaris (Lima bean)
> Epot.cut  -  Solanum tuberosum (Pototoe)
> Epse.cut  -  Pseudomonas sp.
> Erab.cut  -  Oryctolagus sp. (Rabbit)
> Erat.cut  -  Rattus sp. (Rat)
> Erhm.cut  -  Rhizobium meliloti
> Eric.cut  -  Oryza sativa (Rice)
> Eshp.cut  -  Ovis sp. (Sheep)
> Eslm.cut  -  Physarum polycephalum
> Esoy.cut  -  Glycine max (Soybean)
> Esta.cut  -  Staphylococcus aureus
> Esty.cut  -  Salmonella thphimurium
> Esus.cut  -  Strongylocentrotus purpuratus
> Etob.cut  -  Nicotiana tabacum (Tobacco)
> Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
> Etom.cut  -  Lycopersicon esculentum (Tomato)
> Etrb.cut  -  Trypanosoma brucei
> Ewht.cut  -  Triticum aestivum (Wheat)
> Exel.cut  -  Xenopus laevis
> Eysc.cut  -  Saccharomyces cerevisiae
> Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
> Eysp.cut  -  Schizosaccharomyces pombe
> 
>  
> ----- Original Message ----- 
> 
>         From: Carole Louis
>         To: Liste Emboss
>         Sent: Tuesday, March 09, 2004 4:05 PM
>         Subject: [EMBOSS] CUTG
>         
>         Hi,
>         
>         I extracted the CUTG database with cutgextract without any
>         problem but I'd like to have a more explicite name for my .cut
>         files ? Is it possible to obtain it ?
>         
>         Thanks,
>         
>         -- 
>         Carole Louis <louis at gtptech.com>
>         GTP Technology 

-- 
Carole Louis <louis at gtptech.com>
GTP Technology

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From louis at gtptech.com  Wed Mar 10 09:34:23 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 10:34:23 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
Message-ID: <1078911263.3235.33.camel@Coriandre>

Hi Graziano and thank you.

I'm looking for the table of Spodoptera frugiperda. I thought it was
Espo.cut but this table seems to be very different from that I found on
this internet site :   http://www.kazusa.or.jp/codon/.
Does anybody know which table is the one I need ?

Thanks,
Carole


Le mar 09/03/2004 ? 16:17, Graziano P. a ?crit :

> ? 
> Hi Carol,
> not every file but most are described in the README file from
> ftp://ftp.ebi.ac.uk/pub/databases/codonusage. Below I report the list
> I am using.
>  
> Regards
> Graziano
>  
> Easn.cut  -  Aspergillus nidulans
> Eath.cut  -  Arabidopsis thaliana
> Ebly.cut  -  Hordeum vulgare (Barley)
> Ebmo.cut  -  Bombyx mori (Silk Moth)
> Ebov.cut  -  Bos taurus (Cow)
> Ebsu.cut  -  Bacillus subtilis
> Ecel.cut  -  Caenorhabditis elegans
> Echi.cut  -  Chironomus sp.
> Echk.cut  -  Gallus sp. (Chicken)
> Eddi.cut  -  Dictyostelium discoideum
> Edro.cut  -  Drosophila melanogaster
> Eeco.cut  -  Escherichia coli
> Eham.cut  -  Cricetulus sp. & Mesocricetus sp.(Hamster)
> Ehum.cut  -  Homo sapiens
> Ekpn.cut  -  Klebsiella pneumoniae
> Emac.cut  -  Macaca sp
> Emus.cut  -  Mus sp. (Mouse)
> Emze.cut  -  Zea mays (Maize)
> Emzecp.cut  -  Zea mays chloroplast (Maize)
> Eneu.cut  -  Neurospora crassa
> Engo.cut  -  Neisseria gonorrheae
> Epea.cut  -  Pisum sativum (Pea)
> Epet.cut  -  Petunia sp.
> Epfa.cut  -  Plasmodium falciparum
> Ephv.cut  -  Phaseolus vulgaris (Lima bean)
> Epot.cut  -  Solanum tuberosum (Pototoe)
> Epse.cut  -  Pseudomonas sp.
> Erab.cut  -  Oryctolagus sp. (Rabbit)
> Erat.cut  -  Rattus sp. (Rat)
> Erhm.cut  -  Rhizobium meliloti
> Eric.cut  -  Oryza sativa (Rice)
> Eshp.cut  -  Ovis sp. (Sheep)
> Eslm.cut  -  Physarum polycephalum
> Esoy.cut  -  Glycine max (Soybean)
> Esta.cut  -  Staphylococcus aureus
> Esty.cut  -  Salmonella thphimurium
> Esus.cut  -  Strongylocentrotus purpuratus
> Etob.cut  -  Nicotiana tabacum (Tobacco)
> Etobcp.cut  -  Nicotiana tabacum chloroplast (Tobacco)
> Etom.cut  -  Lycopersicon esculentum (Tomato)
> Etrb.cut  -  Trypanosoma brucei
> Ewht.cut  -  Triticum aestivum (Wheat)
> Exel.cut  -  Xenopus laevis
> Eysc.cut  -  Saccharomyces cerevisiae
> Eyscmt.cut  -  Saccharomyces cerevisiae mitochondrion
> Eysp.cut  -  Schizosaccharomyces pombe
> 
>  
> ----- Original Message ----- 
> 
>         From: Carole Louis
>         To: Liste Emboss
>         Sent: Tuesday, March 09, 2004 4:05 PM
>         Subject: [EMBOSS] CUTG
>         
>         Hi,
>         
>         I extracted the CUTG database with cutgextract without any
>         problem but I'd like to have a more explicite name for my .cut
>         files ? Is it possible to obtain it ?
>         
>         Thanks,
>         
>         -- 
>         Carole Louis <louis at gtptech.com>
>         GTP Technology 

-- 
Carole Louis <louis at gtptech.com>
GTP Technology

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From pmr at ebi.ac.uk  Wed Mar 10 09:29:16 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 10 Mar 2004 09:29:16 +0000
Subject: [EMBOSS] CUTG
In-Reply-To: <1078907483.3235.21.camel@Coriandre>
References: <1078844731.3235.6.camel@Coriandre>	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN> <1078907483.3235.21.camel@Coriandre>
Message-ID: <404EDFEC.1080407@ebi.ac.uk>

Carole Louis wrote:

> Thank you. I'm looking for Spodoptera frugiperda. I thought it was
> Espo.cut but it seems very different of the table I found at
> http://www.kazusa.or.jp/codon/. 

Spo.cut would be Schizosaccharomyces pombe.

After you run cutgextract on the cutg database from 
ftp.ebi.ac.uk/pub/databases/cutg you should have 
ESpodoptera_frugiperda.cut which comes from the gbinv.codons file.

The kazusa service looks interesting ... I wonder whether EMBOSS could 
read codon usage tables directly from there on request... I will try to 
make that work if there is enough interest.

>>----- Original Message ----- 
>>        From: Carole Louis
>>        To: Liste Emboss
>>        
>>        I extracted the CUTG database with cutgextract without any
>>        problem but I'd like to have a more explicite name for my .cut
>>        files ? Is it possible to obtain it ?

We are working on improving the naming and descriptions of codon usage 
files - for EMBOSS 2.9.0. This will have to include cutgextract output.

Does anyone need the codon usage files included in the EMBOSS 
distribution? We would like to "retire" the old ones (the long names) 
and rename (and update) the cutg ones.

regards,

Peter Rice



From louis at gtptech.com  Wed Mar 10 10:17:59 2004
From: louis at gtptech.com (Carole Louis)
Date: 10 Mar 2004 11:17:59 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <404EDFEC.1080407@ebi.ac.uk>
References: <1078844731.3235.6.camel@Coriandre>
	 <010801c405e9$a23ea5b0$18105709@JTCDOMAIN>
	 <1078907483.3235.21.camel@Coriandre>  <404EDFEC.1080407@ebi.ac.uk>
Message-ID: <1078913877.3235.39.camel@Coriandre>

Thanks. I think it's a good idea to read codon usage tables directly on
kasuka website. 

Le mer 10/03/2004 ? 10:29, Peter Rice a ?crit :

> Carole Louis wrote:
> 
> > Thank you. I'm looking for Spodoptera frugiperda. I thought it was
> > Espo.cut but it seems very different of the table I found at
> > http://www.kazusa.or.jp/codon/. 
> 
> Spo.cut would be Schizosaccharomyces pombe.
> 
> After you run cutgextract on the cutg database from 
> ftp.ebi.ac.uk/pub/databases/cutg you should have 
> ESpodoptera_frugiperda.cut which comes from the gbinv.codons file.
> 
> The kazusa service looks interesting ... I wonder whether EMBOSS could 
> read codon usage tables directly from there on request... I will try to 
> make that work if there is enough interest.
> 
> >>----- Original Message ----- 
> >>        From: Carole Louis
> >>        To: Liste Emboss
> >>        
> >>        I extracted the CUTG database with cutgextract without any
> >>        problem but I'd like to have a more explicite name for my .cut
> >>        files ? Is it possible to obtain it ?
> 
> We are working on improving the naming and descriptions of codon usage 
> files - for EMBOSS 2.9.0. This will have to include cutgextract output.
> 
> Does anyone need the codon usage files included in the EMBOSS 
> distribution? We would like to "retire" the old ones (the long names) 
> and rename (and update) the cutg ones.
> 
> regards,
> 
> Peter Rice

-- 
Carole Louis <louis at gtptech.com>
GTP Technology
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From gbottu at ben.vub.ac.be  Wed Mar 10 10:46:29 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Wed, 10 Mar 2004 11:46:29 +0100
Subject: [EMBOSS] CUTG
In-Reply-To: <404EDFEC.1080407@ebi.ac.uk>
References: <1078844731.3235.6.camel@Coriandre> <010801c405e9$a23ea5b0$18105709@JTCDOMAIN> <1078907483.3235.21.camel@Coriandre> <404EDFEC.1080407@ebi.ac.uk>
Message-ID: <20040310104629.GB18868@bigben.ulb.ac.be>

On Wed, Mar 10, 2004 at 09:29:16AM +0000, Peter Rice wrote:
> We are working on improving the naming and descriptions of codon usage 
> files - for EMBOSS 2.9.0. This will have to include cutgextract output.
> 
> Does anyone need the codon usage files included in the EMBOSS 
> distribution? We would like to "retire" the old ones (the long names) 
> and rename (and update) the cutg ones.

Well, there are certainly a number of things that could be done to improve 
codon usage file support in EMBOSS. I would suggest :

- let any program that handles codon usage files read in user provided
files and/or write files in several formats (as is already done for
sequences and features) : CUTG, Staden, GCG, ... 
- for the EMBOSS included files : remove redundant files (why Eeco.cut and 
Eecoli.cut ?,...), provide clear information about which is which, 
update...
 - for CUTG, let cutgextract write file names based on the ID rather then 
the species name. This would provide names that are shorter and free from 
special characters.
- still for CUTG, a system to retrieve a file over the Internet from the 
distribution site is certainly interesting, but so is a way to retrieve it 
from a local SRS (with getz).
Note by the way that CUTG has a drawback : it has a table for each 
organism without making the distinction between different gene 
populations.

	Guy Bottu,
	Belgian EMBnet Node


From khoueiry at ibsm.cnrs-mrs.fr  Thu Mar 11 14:44:32 2004
From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre)
Date: Thu, 11 Mar 2004 15:44:32 +0100
Subject: [EMBOSS] uninstalling Emboss
Message-ID: <40507B50.204@ibsm.cnrs-mrs.fr>

Hi,
I want ot know the best way to uninstall Emboss from my Linux/Debian 
machine. In fact i install it using the tarball.
any suggesting thanks in advance
-- 

---------------------------------
Pierre Khoueiry	
khoueiry at ibsm.cnrs-mrs.fr
LCB - CNRS
31, Chemin Joseph Aiguier,
13402 Marseille CEDEX 20, France
---------------------------------




From kim at inb.uni-luebeck.de  Thu Mar 11 16:42:59 2004
From: kim at inb.uni-luebeck.de (Jan T. Kim)
Date: Thu, 11 Mar 2004 17:42:59 +0100
Subject: [EMBOSS] uninstalling Emboss
In-Reply-To: <40507B50.204@ibsm.cnrs-mrs.fr>; from khoueiry@ibsm.cnrs-mrs.fr on Thu, Mar 11, 2004 at 03:44:32PM +0100
References: <40507B50.204@ibsm.cnrs-mrs.fr>
Message-ID: <20040311174258.E17507@pc10.inb.mu-luebeck.de>

On Thu, Mar 11, 2004 at 03:44:32PM +0100, KHOUEIRY pierre wrote:

> I want ot know the best way to uninstall Emboss from my Linux/Debian 
> machine. In fact i install it using the tarball.
> any suggesting thanks in advance

Since the make process of the EMBOSS package is built with the autoconf
and automake standard tool suite, there is an uninstall target which
you can use for uninstalling. I.e. go to the EMBOSS source directory
where you ran ``make install'', and run ``make uninstall'' there.
If you don't have that source directory anymore, you could unpack the
tarball once more and run the ./configure script with exactly the
same parameters as you did for installing.

Greetinx, Jan
-- 
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: kim at inb.uni-luebeck.de                          |
 |    *NEW*    WWW:   http://www.inb.uni-luebeck.de/staff/kim.html    |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*


From Paul.Baumgartner at unibas.ch  Thu Mar 11 16:48:04 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Thu, 11 Mar 2004 17:48:04 +0100
Subject: [EMBOSS] MacOSXPanther
Message-ID: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>

During compilation of emboss 2.8.0-2 the process stopped with this 
comment :
......................
checking if java include directory given... yes
Java directory /Library/Java/Home exists
checking for javac... yes
checking if java OS include directory given... yes
Javaos directory /Library/Java/Home/include does not exist
make
make: *** No targets specified and no makefile found.  Stop.
### execution of make failed, exit code 2
Failed: compiling emboss-2.8.0-2 failed

a problem by Java ?

(all other packages (e.g. rasmol) compiled perfect)
Thanks to suggestions
Paul



From ableasby at hgmp.mrc.ac.uk  Thu Mar 11 18:14:35 2004
From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby)
Date: Thu, 11 Mar 2004 18:14:35 GMT
Subject: [EMBOSS] MacOSXPanther
Message-ID: <200403111814.i2BIEZHg017285@bromine.hgmp.mrc.ac.uk>

The SDK component of Java isn't installed from the CD by default.
It is on your 3rd Panther CD though.

HTH

Alan Bleasby
RFCGR


From kvddrift at earthlink.net  Thu Mar 11 22:56:06 2004
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Thu, 11 Mar 2004 17:56:06 -0500
Subject: [EMBOSS] MacOSXPanther
In-Reply-To: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>
References: <DDB01599-737B-11D8-B17B-003065B9531E@unibas.ch>
Message-ID: <47756100-73AF-11D8-A878-003065A5FDCC@earthlink.net>


On Mar 11, 2004, at 11:48 AM, Paul Baumgartner wrote:

> a problem by Java ?
>
> (all other packages (e.g. rasmol) compiled perfect)
> Thanks to suggestions
>

You need to install the Java SDK, this is not installed by default. See 
the fink website (fink.sf.net).


- Koen.



From fernan at iib.unsam.edu.ar  Mon Mar 15 16:51:05 2004
From: fernan at iib.unsam.edu.ar (Fernan Aguero)
Date: Mon, 15 Mar 2004 13:51:05 -0300
Subject: [EMBOSS] Bug in fuzznuc output?
Message-ID: <20040315165105.GD45860@iib.unsam.edu.ar>

Hi!

I'm searching for a nucleic acid pattern in a set of
sequences. The sequences are in a multiple fasta file, and
I'm searching for the pattern in both strands.

While testing my searches and adjusting the number of
mismatches that I would allow, I noticed that in the
standard output format, if the pattern matches in the
reverse strand, then Start > End (i.e. the position in the
sequence where the pattern begins is given with respect to
the plus strand).

Now, for my work I need to have the output in an easy to
parse format. But if I choose to have the output in
tab-delimited form (-rformat excel), then the Start and End
positions are always (i.e. in all cases) shown with Start <
End. Thus, there is no way to tell which are the cases of
matches to the reverse strand.

Is this an already known issue?

Since we are already here, let's go for a few suggestions:
in the standard output format (seqtable), there is a header
which includes the program, rundate, report format, etc. It
seems to me that this header is there to summarize global
info about the fuzznuc run.

Then, for each sequence analyzed the report shows the
pattern, the number of mismatches allowed, the number of
hits, and whether or not the complementary strand has been
searched. At least for me, there is unnecessary repetition.

For example: in all cases we have look for the same pattern,
allowing for the same number of mismatches and asking to
search also on the reverse strand. So why not put these
runtime values in the header, and avoid the repetition?

Also, why not report if the match was on the forward or
reverse strand _for each sequence_? (I mean, to make it more
clear, and not just let the user note that Start > End).

Thanks in advance,

Fernan

PS: BTW, I'm running EMBOSS-2.6.0 on FreeBSD-4.9

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan


From stefanie.debodt at psb.ugent.be  Tue Mar 16 17:51:00 2004
From: stefanie.debodt at psb.ugent.be (Stefanie De Bodt)
Date: Tue, 16 Mar 2004 18:51:00 +0100
Subject: [EMBOSS] seqret
Message-ID: <40573E84.4050305@psb.ugent.be>

Dear,

I am using the EMBOSS program SEQRET to retrieve sequences in EMBL 
format out a local EMBL database. Retrieving embl formatted sequences 
works. On your web site, I found an option, -feature, which allows 
additional information to be included in the embl result file. This 
however didn?t work, not in interactive mode and not using the following 
command line

seqret -feature -sequence DBname:AC -outseq embl:AC.embl

I get several warnings and I can?t figure out what the reason for these 
warnings is.

Warning: bad /cons_splice value '(5'site:YES,'
Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'
Warning: RICAMYBA: Bad value '(5'site:no,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'
Warning: RICAMYBB: Bad value '(5'site:no,' for tag '/cons_splice'
Warning: bad /cons_splice value '(5'site:no,'

Could you help me with this problem, is there a mistake in the command 
line or is it due to something else?

Best regards,

Stefanie De Bodt

-- 
Stefanie De Bodt
Research Group of Bioinformatics and Evolutionary Genomics
Department of Plant Systems Biology
Ghent University - Flemish Institute for Biotechnology (VIB)
Technologiepark 927, B-9052 Ghent, BELGIUM

Tel: +32 (0)9 3313692
Fax: +32 (0)9 3313809

stefanie.debodt at psb.ugent.be
http://www.psb.ugent.be/bioinformatics




From pmr at ebi.ac.uk  Tue Mar 16 18:05:50 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 16 Mar 2004 18:05:50 +0000
Subject: [EMBOSS] seqret
In-Reply-To: <40573E84.4050305@psb.ugent.be>
References: <40573E84.4050305@psb.ugent.be>
Message-ID: <405741FE.4020000@ebi.ac.uk>

Stefanie De Bodt wrote:

> seqret -feature -sequence DBname:AC -outseq embl:AC.embl
> 
> I get several warnings and I can?t figure out what the reason for these 
> warnings is.
> 
> Warning: bad /cons_splice value '(5'site:YES,'
> Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
> 
> Could you help me with this problem, is there a mistake in the command 
> line or is it due to something else?

EMBOSS validates the EMBL feature table syntax, using a reasonably 
up-to-date version of the EMBL feature table document (I do have some 
minor updates to add for the latest version).

Is this your own database, or is this an EMBL entry?

These are only warnings ... but I would be interested to see the output 
of entret (the complete text of the entry as read by EMBOSS) to check 
the feature validation is correct.

regards,

Peter Rice



From stefanie.debodt at psb.ugent.be  Tue Mar 16 18:21:16 2004
From: stefanie.debodt at psb.ugent.be (Stefanie De Bodt)
Date: Tue, 16 Mar 2004 19:21:16 +0100
Subject: [EMBOSS] seqret
In-Reply-To: <405741FE.4020000@ebi.ac.uk>
References: <40573E84.4050305@psb.ugent.be> <405741FE.4020000@ebi.ac.uk>
Message-ID: <4057459C.1090303@psb.ugent.be>



Peter Rice wrote:

> Stefanie De Bodt wrote:
>
>> seqret -feature -sequence DBname:AC -outseq embl:AC.embl
>>
>> I get several warnings and I can?t figure out what the reason for 
>> these warnings is.
>>
>> Warning: bad /cons_splice value '(5'site:YES,'
>> Warning: PVU13023: Bad value '(5'site:YES,' for tag '/cons_splice'
>>
>> Could you help me with this problem, is there a mistake in the 
>> command line or is it due to something else?
>
>
> EMBOSS validates the EMBL feature table syntax, using a reasonably 
> up-to-date version of the EMBL feature table document (I do have some 
> minor updates to add for the latest version).
>
> Is this your own database, or is this an EMBL entry?

I downloaded the database just recently from the NCBI FTP site. It is 
the database that contains all plant nucleotide sequences.

>
> These are only warnings ... but I would be interested to see the 
> output of entret (the complete text of the entry as read by EMBOSS) to 
> check the feature validation is correct.

Indeed, only warnings.The output file seems OK. I have attached it.

thanks,

Stefanie De Bodt

>
> regards,
>
> Peter Rice
>
>

-- 
Stefanie De Bodt
Research Group of Bioinformatics and Evolutionary Genomics
Department of Plant Systems Biology
Ghent University - Flemish Institute for Biotechnology (VIB)
Technologiepark 927, B-9052 Ghent, BELGIUM

Tel: +32 (0)9 3313692
Fax: +32 (0)9 3313809

stefanie.debodt at psb.ugent.be
http://www.psb.ugent.be/bioinformatics

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From EliminateBugs at bestholidaygifts01.com  Tue Mar 16 18:50:22 2004
From: EliminateBugs at bestholidaygifts01.com (CarsAmerica.com)
Date: Tue, 16 Mar 2004 21:50:22 +0300
Subject: [EMBOSS] Want a New Car?
Message-ID: <idg077Bidgfi1A0ut@bestholidaygifts01.com>

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From d.gatherer at vir.gla.ac.uk  Wed Mar 17 16:34:31 2004
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Wed, 17 Mar 2004 16:34:31 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <5.2.1.1.1.20030930111106.00b14960@udcf.gla.ac.uk>
Message-ID: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>

Hi

Is there an esim4 man page?

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html

The rest of EMBASSY is above, but not esim4.  The original sim4 has a quick 
help list, but I wondered if there is any extra functionality in the 
EMBASSY version.

Cheers
Derek

 > sim4
sim4 seq1 seq2_db [[WXKCRDHAPNBS]=]

        W  -  word size. (W=12)
        X  -  value for terminating word extensions. (X=12)
        K  -  MSP score threshold for the first pass. (e.g., K=16)
        C  -  MSP score threshold for the second pass. (e.g., C=12)
        R  -  direction of search; 0 - search the '+' (direct) strand only;
              1 - search the '-' strand only; 2 - search both strands and
              report the best match. (R=2)
        D  -  bound for the range of diagonals within consecutive msps in an
              exon. (D=10)
        H  -  weight factor for MSP scores in relinking. (H=500)
        A  -  output format: exon endpoints only (A=0), alignment text (A=1),
              alignment in lav (block) format (A=2), or both exon endpoints
              and alignment text (A=3, A=4). If complement match, A=0,1,2,3
              give direct positions in the long sequence and complement
              positions in the short sequence. A=4 gives direct positions in
              the first sequence, regardless of the relative lengths.
              A=5 prints the exon and CDS coordinates (the latter, if known)
              in the `exon file' format required by PipMaker. To be used
              with full-length mRNA sequences.
        P  -  if not 0, remove poly-A tails; report coordinates in the
              '+' (direct) strand for complement matches; use lav alignment
              headers in all display options. (P=0)
        N  -  accuracy of sequences (non-zero for highly accurate). (N=0)
        B  -  if 0, dis-allow ambiguity codes (other than N and X) in the
              sequence data. (B=1)
        S  -  coding region specification (available only with A=5);
              format: S=n1..n2



From mathog at mendel.bio.caltech.edu  Wed Mar 17 16:44:03 2004
From: mathog at mendel.bio.caltech.edu (David Mathog)
Date: Wed, 17 Mar 2004 08:44:03 -0800
Subject: [EMBOSS] esim4 man page
Message-ID: <E1B3e9D-0001qC-00@mendel.bio.caltech.edu>

> Is there an esim4 man page?

I don't recall writing one.  esim4 -h will list the command line
options and what they do, to the extent that could be decipered
from the original source code.

Regards,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


From d.m.a.martin at dundee.ac.uk  Wed Mar 17 17:03:06 2004
From: d.m.a.martin at dundee.ac.uk (David Martin)
Date: Wed, 17 Mar 2004 17:03:06 +0000
Subject: [EMBOSS] Problems retrieving from uniprot by id
Message-ID: <BC7E354A.FF39%d.m.a.martin@dundee.ac.uk>

Using EMBOSS 2.8.0 I am trying to retrieve from Uniprot by ID without
success. This is using the Swissprot

I have indexed appropriately ( using fields as described on the emboss
documentation.)

I can retrieve by accession number but cannot retrieve the same sequence by
id. 

I have run the program with -debug and get the following:

ajFileNewIn '/mn/proteas/u1/davidm/entrynam.idx'
seqCdReadHeader file /mn/proteas/u1/davidm/entrynam.idx
  FileSize: 2912040 NRecords: 145587 recsize: 20 idsize: 10
seqCdFileOpen '/mn/proteas/u1/davidm/entrynam.idx' NRecords: 145587 RecSize:
20
entry id: 'tf_human' acc: ''
entry id: 'tf_human' acc: ''
seqCdIdxSearch (entry 'tfz_human') records: 145587
idx test 72793 'NUYM_HUMAN'  1 (+/- 145586)
idx test 109190 'SYFA_SULTO'  1 (+/- 72792)
idx test 127388 'Y06C_BPT4' -1 (+/- 36395)
idx test 118289 'UAP1_ARATH' -1 (+/- 18196)
idx test 113739 'THS1_ARAHY' -1 (+/- 9097)
idx test 111464 'TAR5_HUMAN'  1 (+/- 4547)
idx test 112601 'TERT_OXYTR'  1 (+/- 2273)
idx test 113170 'THI1_CORNE' -1 (+/- 1136)
idx test 112885 'TGF2_RAT' -1 (+/- 567)
idx test 112743 'TFB1_THEVO'  1 (+/- 282)
idx test 112814 'TFPI_HUMAN'  1 (+/- 140)
idx test 112849 'TFZ_DROME'  1 (+/- 69)
idx test 112867 'TGF1_BOVIN' -1 (+/- 34)
idx test 112858 'TGA5_ARATH' -1 (+/- 16)
idx test 112853 'TG37_MOUSE' -1 (+/- 7)
idx test 112851 'TG21_TOBAC' -1 (+/- 2)
idx test 112850 'TFZ_HUMAN'  0 (+/- 0)
EMBLCD Entry failed
Database Entry 'tf_human' not found
seqCdQryClose clean up qryd
seqCdFileClose of /mn/proteas/u1/davidm/entrynam.idx
closing file '/mn/proteas/u1/davidm/entrynam.idx'
seqCdFileClose of /mn/proteas/u1/davidm/division.lkp
closing file '/mn/proteas/u1/davidm/division.lkp'
Database 'sw' : access method 'emblcd' failed

It might be an 'off by one' error in the  search or the indexing.
searching for tfz_human behaves appropriately.

..d

-- 
David Martin PhD <david at compbio.dundee.ac.uk>
Post-Genomics and Molecular Interactions Centre
University of Dundee




From EliminateBugs at special-deal0001.com  Thu Mar 18 00:22:27 2004
From: EliminateBugs at special-deal0001.com (Reduce Body Fat)
Date: Thu, 18 Mar 2004 03:22:27 +0300
Subject: [EMBOSS] Accelerate Weight Loss
Message-ID: <idg077Bidgfi1A0ut@special-deal0001.com>

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From stefanielager at fastmail.ca  Thu Mar 18 06:08:45 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 18 Mar 2004 06:08:45 +0000 (UTC)
Subject: [EMBOSS] esim4 man page
In-Reply-To: <E1B3e9D-0001qC-00@mendel.bio.caltech.edu>
Message-ID: <20040318060846.CB20C861C92@mail.interchange.ca>

ESIM4 doesn't seem to be able to align multiple mRNA sequences to a
single genomic sequence, which sim4 as an external program can. In
version 2.8.0 of emboss ESIM4 alignments don't work (format=3), it finds
the correct reagion to align, but it seems to "extract" the wrong
genomic region to make the alignment (it was OK in version 2.6.0 of
EMBOSS). 

Stefanie

>> Is there an esim4 man page?
> 
> I don't recall writing one.  esim4 -h will list the command line
> options and what they do, to the extent that could be decipered
> from the original source code.
> 
> Regards,
> 
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From pmr at ebi.ac.uk  Thu Mar 18 10:06:41 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Mar 2004 10:06:41 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <20040318060846.CB20C861C92@mail.interchange.ca>
References: <20040318060846.CB20C861C92@mail.interchange.ca>
Message-ID: <405974B1.8070507@ebi.ac.uk>

Stefanie Lager wrote:

> ESIM4 doesn't seem to be able to align multiple mRNA sequences to a
> single genomic sequence, which sim4 as an external program can. In
> version 2.8.0 of emboss ESIM4 alignments don't work (format=3), it finds
> the correct reagion to align, but it seems to "extract" the wrong
> genomic region to make the alignment (it was OK in version 2.6.0 of
> EMBOSS). 

Thanks for pointing that out.

I am working on QA tests for the EMBASSY programs and will put these 
test cases in.

regards,

Peter Rice



From pmr at ebi.ac.uk  Thu Mar 18 10:05:28 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 18 Mar 2004 10:05:28 +0000
Subject: [EMBOSS] esim4 man page
In-Reply-To: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>
References: <5.2.1.1.1.20040317163127.033dfde0@udcf.gla.ac.uk>
Message-ID: <40597468.2000801@ebi.ac.uk>

Derek Gatherer wrote:

> Hi
> 
> Is there an esim4 man page?
> 
> http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html
> 
> The rest of EMBASSY is above, but not esim4.  The original sim4 has a 
> quick help list, but I wondered if there is any extra functionality in 
> the EMBASSY version.

As it happens, I am working through the EMBASSY programs that don't have 
man pages - hmmer is also missing.

They will appear soon.

regards,

Peter Rice



From sandeepd at persistent.co.in  Thu Mar 18 13:18:06 2004
From: sandeepd at persistent.co.in (sandeepd at persistent.co.in)
Date: Thu, 18 Mar 2004 18:48:06 +0530
Subject: [EMBOSS] Blocked delivery of your email to chitra@pspl.co.in
Message-ID: <200403181318.i2IDI8VK008989@smtp.pspl.co.in>

                 BLOCKED DELIVERY OF YOUR EMAIL TO chitra at pspl.co.in 

Your email has been stopped for reasons stated at the bottom of this mail.

If your message is HTML/RichText and wrongly reported as SPAM below 
send the email again in plain-text format. 

If your message is reported to have virus, please check your system 
for virii and clean it up. 

If you still think that your message is free of all the above, please 
report it to postmaster at persistent.co.in or sysads at persistent.co.in. 


Email was blocked due to the presence of a virus
	Comment: Virus detected in the mail

/unpacked/mp3music.pif - Win32/Netsky.D worm


End.


From LendersCompete at bargains001.com  Sat Mar 20 12:38:58 2004
From: LendersCompete at bargains001.com (Lenders Compete)
Date: Sat, 20 Mar 2004 15:38:58 +0300
Subject: [EMBOSS] Low Rates, Trusted Lenders
Message-ID: <idg077Bidgfi1A0ut@bargains001.com>

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From antivirus at unito.it  Sat Mar 20 14:28:37 2004
From: antivirus at unito.it (antivirus at unito.it)
Date: Sat, 20 Mar 2004 15:28:37 +0100
Subject: [EMBOSS] - DO NOT REPLY - Inflex scan report [0320152824368]
Message-ID: <200403201428.i2KESb7j024400@albert.unito.it>

Administrator Email Reply Address: rete at unito.it
Email sent to:  sergio.castellano at unito.it
Inflex ID: 0320152824368
Report Details -----------------------------------------------
AntiVirus Results...

File NAME/TYPE Scan Results
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0320152824368  from:emboss at embnet.org  to: sergio.castellano at unito.it
END OF MESSAGE.

End.
.


From georg.otto at tuebingen.mpg.de  Mon Mar 22 21:34:58 2004
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Mon, 22 Mar 2004 22:34:58 +0100
Subject: [EMBOSS] eprimer3
Message-ID: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>

Hi,

I have problems using eprimer3. It seems to me that it can?t take 
multiple sequence files as an input (I tried with a multiple fasta file 
and a file in EMBL format). However primer3 itself can take multiple 
sequences. Is there something I missed?

Best regards,

Georg


From stefanielager at fastmail.ca  Tue Mar 23 06:53:52 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Tue, 23 Mar 2004 06:53:52 +0000 (UTC)
Subject: [EMBOSS] eprimer3
Message-ID: <20040323065416.8A9D8865D28@mail.interchange.ca>

I haven?t used eprimer3 extensively, but for version 2.8.0 of EMBOSS
eprimer3 can take multiple fasta sequence files as input, and it designs
primers for all input sequences.

Stefanie

> Hi,
> 
> I have problems using eprimer3. It seems to me that it can?t take
> multiple sequence files as an input (I tried with a multiple fasta
> file and a file in EMBL format). However primer3 itself can take
> multiple sequences. Is there something I missed?
> 
> Best regards,
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From henrikki.almusa at helsinki.fi  Tue Mar 23 07:15:04 2004
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Tue, 23 Mar 2004 09:15:04 +0200
Subject: [EMBOSS] eprimer3
In-Reply-To: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>
References: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de>
Message-ID: <200403230915.04470.henrikki.almusa@helsinki.fi>

On Monday 22 March 2004 23:34, Georg Otto wrote:
> Hi,
>
> I have problems using eprimer3. It seems to me that it can?t take
> multiple sequence files as an input (I tried with a multiple fasta file
> and a file in EMBL format). However primer3 itself can take multiple
> sequences. Is there something I missed?

Mail from archives:

----

[EMBOSS] eprimer3: max input file number?
Date: 21.10.2003 19:41
From: Iain Drummond <idrummon at receptor.mgh.harvard.edu>

I have run into a limitation using eprimer3 as an interface for primer3. It
seems that eprimer3 will accept up to 23 sequences (in a single fasta
formatted text file) but not 24 or more; with 24 or more sequences, eprimer3
and primer3_core will just hang as ?sleeping? processes and never finish. My
goal is to automate genomic sequence analysis (zebrafish) in order to
generate new, potentially useful polymorphic markers from dinucleotide
repeats. eprimer3 is the last step where a long list of ~500 bp sequences
are sent to primer3 to make primers.

-----

And reply to above:

-----

Re: [EMBOSS] maximum number of sequences for eprimer3
Date: 22.10.2003 22:06
From: Alan Bleasby <ableasby at hgmp.mrc.ac.uk>

Having had a quick look at the code I suspect that it is not
a variable involved (EMBOSS programs are designed not to be
limited in that way, usually only by system resource available).
 
The code uses pipes to redirect stdin and stdout to/from primer3_core.
A possible cause is therefore blocking from a full buffer. I'll
let the author of the eprimer3 program know about it.

HTH

Alan

----

-- 
Henrikki Almusa


From pscotney at hotmail.com  Tue Mar 23 07:16:41 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Tue, 23 Mar 2004 18:16:41 +1100
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
Message-ID: <Sea2-F29qNHKEn8diHN0000c39a@hotmail.com>


Hello,

I am having problems installing EMBOSS and Jemboss.  I have read all the 
INSTALL and README docs in the EMBOSS-2.8.0 directory and the web docs for 
Jemboss standalone installation, so please no RTFM responses :)

I am building EMBOSS-2.8.0 on a GNU/Linux system (Mandrake 9.1) with 
Blackdown Java j2sdk-1.3.1-02b-FCS-linux-i386 installed and running ok.  I 
have installed zlib-1.2.1 libpng-1.2.5 and gd-2.0.22 so all the libraries 
and includes are present.

I build as root with the following commands:

cd EMBOSS-2.8.0
./configure --prefix=/usr/local/emboss
make
make install
cd jemboss/utils
./install-jemboss-server.sh

selecting the option (2) STANDALONE and the rest of the prompts.  The 
generated /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh and 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties files 
all look ok with the correct paths.

I have added /usr/local/emboss/{bin,lib} to the PATH and ld.so.conf 
respectively and wosname -auto is working:

ALIGNMENT CONSENSUS
cons             Creates a consensus from multiple alignments
megamerger       Merge two large overlapping nucleic acid sequences
merger           Merge two overlapping nucleic acid sequences
etc.....

but when I

cd /usr/local/emboss/share/EMBOSS/jemboss
./runJemboss.sh

all I ever get is the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: 
org/emboss/jemboss/Jemboss

What have I done wrong?  Please help!

Regards

Pierre


--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
SEEK: Now with over 50,000 dream jobs! Click here:  
http://ninemsn.seek.com.au?hotmail



From tcarver at rfcgr.mrc.ac.uk  Tue Mar 23 08:26:07 2004
From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver)
Date: Tue, 23 Mar 2004 08:26:07 +0000 (GMT)
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
In-Reply-To: <Sea2-F29qNHKEn8diHN0000c39a@hotmail.com>
Message-ID: <Pine.SOL.4.44.0403230823410.5931-100000@uranium>

Hi Pierre

The problem is likely to be that you precompiled emboss before running
the install script. There is no need, the install script does this for
you with the correct java flags. Try a 'make clean' and then run the
install script.

Hope this helps.
Regards
Tim Carver

RFCGR

>
> I am building EMBOSS-2.8.0 on a GNU/Linux system (Mandrake 9.1) with
> Blackdown Java j2sdk-1.3.1-02b-FCS-linux-i386 installed and running ok.  I
> have installed zlib-1.2.1 libpng-1.2.5 and gd-2.0.22 so all the libraries
> and includes are present.
>
> I build as root with the following commands:
>
> cd EMBOSS-2.8.0
> ./configure --prefix=/usr/local/emboss
> make
> make install
> cd jemboss/utils
> ./install-jemboss-server.sh
>
> selecting the option (2) STANDALONE and the rest of the prompts.  The
> generated /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh and
> /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties files
> all look ok with the correct paths.
>
> I have added /usr/local/emboss/{bin,lib} to the PATH and ld.so.conf
> respectively and wosname -auto is working:
>
> ALIGNMENT CONSENSUS
> cons             Creates a consensus from multiple alignments
> megamerger       Merge two large overlapping nucleic acid sequences
> merger           Merge two overlapping nucleic acid sequences
> etc.....
>
> but when I
>
> cd /usr/local/emboss/share/EMBOSS/jemboss
> ./runJemboss.sh
>
> all I ever get is the following error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/emboss/jemboss/Jemboss
>
> What have I done wrong?  Please help!
>
> Regards
>
> Pierre
>
>
> --
> Dr Pierre Scotney
> Melbourne
> Australia
>
> _________________________________________________________________
> SEEK: Now with over 50,000 dream jobs! Click here:
> http://ninemsn.seek.com.au?hotmail
>



From gwilliam at hgmp.mrc.ac.uk  Tue Mar 23 09:27:58 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Tue, 23 Mar 2004 09:27:58 +0000
Subject: [EMBOSS] eprimer3
References: <C494DF6A-7C48-11D8-973D-003065C99468@tuebingen.mpg.de> <200403230915.04470.henrikki.almusa@helsinki.fi>
Message-ID: <4060031D.E530E8C9@hgmp.mrc.ac.uk>


The 23 input sequence limitation of eprimer3 will be fixed in the next
release.
In the meantime, you could get a copy of the fixed program from:
ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/eprimer3.*

Regards,
Gary

Henrikki Almusa wrote:
> [EMBOSS] eprimer3: max input file number?
> Date: 21.10.2003 19:41
> From: Iain Drummond <idrummon at receptor.mgh.harvard.edu>
> 
> I have run into a limitation using eprimer3 as an interface for primer3. It
> seems that eprimer3 will accept up to 23 sequences (in a single fasta
> formatted text file) but not 24 or more; with 24 or more sequences, eprimer3
> and primer3_core will just hang as ?sleeping? processes and never finish. My
> goal is to automate genomic sequence analysis (zebrafish) in order to
> generate new, potentially useful polymorphic markers from dinucleotide
> repeats. eprimer3 is the last step where a long list of ~500 bp sequences
> are sent to primer3 to make primers.


-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pscotney at hotmail.com  Wed Mar 24 04:13:01 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Wed, 24 Mar 2004 15:13:01 +1100
Subject: [EMBOSS] EMBOSS and Jemboss installation problems
Message-ID: <Sea2-F12rrKJ0gfZe5c0001300f@hotmail.com>


>From: "Dr T. Carver" <tcarver at rfcgr.mrc.ac.uk>
>
>The problem is likely to be that you precompiled emboss before running
>the install script. There is no need, the install script does this for
>you with the correct java flags. Try a 'make clean' and then run the
>install script.

Hi Tim,

I tried make clean and a freshly unpacked source tree but both times when 
executing the install-jemboss-server.sh script with the standalone option 
there is an error in the build phase:

/bin/sh ../../mkinstalldirs /usr/local/emboss/share/EMBOSS/jemboss/lib
/usr/bin/install -c -m 644 README 
/usr/local/emboss/share/EMBOSS/jemboss/lib/README
/usr/bin/install -c -m 644 activation.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/activation.jar
/usr/bin/install -c -m 644 jakarta-regexp-1.2.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar
/usr/bin/install -c -m 644 mail.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/mail.jar
/usr/bin/install -c -m 644 xerces.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/xerces.jar
/usr/bin/install -c -m 644 jalview.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jalview.jar
/usr/bin/install -c -m 644 jcert.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jcert.jar
/usr/bin/install -c -m 644 jnet.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jnet.jar
/usr/bin/install -c -m 644 jsse.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/jsse.jar
/usr/bin/install -c -m 644 JembossPrintAlignment.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/JembossPrintAlignment.jar
/usr/bin/install -c -m 644 grout.jar 
/usr/local/emboss/share/EMBOSS/jemboss/lib/grout.jar
make[4]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/lib'
Making install in org
make[2]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
Making install in emboss
make[3]: Entering directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
Making install in jemboss
make[4]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
Making install in editor
make[5]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make  install-exec-hook
make[7]: Entering directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss
mkdir /usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/editor
/usr/bin/install: cannot stat `*.class': No such file or directory
make[7]: *** [install-exec-hook] Error 1
make[7]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[6]: *** [install-exec-am] Error 2
make[6]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[5]: *** [install-am] Error 2
make[5]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss/editor'
make[4]: *** [install-recursive] Error 1
make[4]: Leaving directory 
`/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss/jemboss'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org/emboss'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss/org'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/pscotney/EMBOSS-2.8.0/jemboss'
make: *** [install-recursive] Error 1

--------------------------------------------------------------

EMBASSY packages can optionally be installed along with
the EMBOSS applications, see:
http://www.uk.embnet.org/Software/EMBOSS/EMBASSY/

--------------------------------------------------------------

Install EMBASSY packages (y,n) [y]?
n

-------------------------- ClustalW --------------------------

To use emma (EMBOSS interface to ClustalW) Jemboss needs to
know the path to the clustalw binary.

Enter the path to clustalw or press return to set
this later in jemboss.properties


-------------------------- Primer3  --------------------------

To use eprimer3 (EMBOSS interface primer3 from the Whitehead
Institute) Jemboss needs to know the path to the primer3_core
binary.

Enter the path to primer3_core or press return to set
this later in jemboss.properties

java.io.FileNotFoundException: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/wossname.jar (No such file 
or directory)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
	at sun.tools.jar.Main.run(Main.java:134)
	at sun.tools.jar.Main.main(Main.java:904)
java.io.FileNotFoundException: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/resources.jar (No such file 
or directory)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:102)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:62)
	at sun.tools.jar.Main.run(Main.java:134)
	at sun.tools.jar.Main.main(Main.java:904)
error: cannot read: 
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
1 error
error: cannot read: 
/usr/local/emboss/share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
1 error
mv: cannot stat 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory
touch: creating 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory
./install-jemboss-server.sh: line 362: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 366: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 367: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 370: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 374: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 375: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 381: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 382: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 383: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 384: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 388: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
./install-jemboss-server.sh: line 389: 
/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties: No such 
file or directory
cp: cannot stat 
`/usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties': No 
such file or directory

Changed /usr/local/emboss/share/EMBOSS/jemboss/resources/jemboss.properties
to reflect this installation (original in jemboss.properties.orig)



sed: can't read /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh: No 
such file or directory
mv: cannot stat `/usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh': No 
such file or directory

To run Jemboss:
cd /usr/local/emboss/share/EMBOSS/jemboss
./runJemboss.sh

lt looks like the editor classes are not being built:

$ ls -R -w 80 jemboss/
jemboss/:
editor		  JembossJarUtil.class	JembossParams.java     parser
FileManager.java  JembossJarUtil.java	Jemboss$winExit.class  programs
gui		  Jemboss.java		Makefile	       server
Jemboss$1.class   JembossLogo.java	Makefile.am	       soap
Jemboss.class	  JembossParams.class	Makefile.in

jemboss/editor:
AlignApplet.java			     Makefile
AlignJFrame.java			     Makefile.am
ColourJFrame.java			     Makefile.in
ColourMenu.java				     Matrix.java
ColourPanel.java			     MatrixJFrame.java
Consensus.java				     PatternJFrame.java
ConsensusOptions.java			     PlotConsensus.java
GraphicSequenceCollection.java		     PrettyPlotJFrame.java
GroutAlignJFrameEvent.java		     PrintableJTable.java
GroutAlignJFrame.java			     PrintAlignmentImage.java
GroutAlignJFrameListener.java		     PrintAlignment.java
GroutGraphicSequenceCollectionEvent.java     Sequence.java
GroutGraphicSequenceCollection.java	     SequenceJPanel.java
GroutGraphicSequenceCollectionListener.java  SequenceNameJButton.java
GroutSequence.java			     SequenceProperties.java
GroutSequenceJPanel.java		     SequenceReader.java
IDTableJFrame.java			     SequenceSaver.java

jemboss/gui:
AdvancedOptions$1.class   Makefile			SetUpMenuBar$10.class
AdvancedOptions$2.class   Makefile.am			SetUpMenuBar$11.class
AdvancedOptions.class	  Makefile.in			SetUpMenuBar$1.class
AdvancedOptions.java	  MemoryComboBox.class		SetUpMenuBar$2.class
Browser.java		  MemoryComboBox.java		SetUpMenuBar$3.class
BuildProgramMenu$1.class  ResultsMenuBar.java		SetUpMenuBar$4.class
BuildProgramMenu$2.class  ScrollPanel.class		SetUpMenuBar$5.class
BuildProgramMenu$3.class  ScrollPanel.java		SetUpMenuBar$6.class
BuildProgramMenu$4.class  sequenceChooser		SetUpMenuBar$7.class
BuildProgramMenu$5.class  SequenceData.class		SetUpMenuBar$8.class
BuildProgramMenu$6.class  SequenceData.java		SetUpMenuBar$9.class
BuildProgramMenu$7.class  SequenceList$1.class		SetUpMenuBar.class
BuildProgramMenu$8.class  SequenceList$2.class		SetUpMenuBar.java
BuildProgramMenu.class	  SequenceList$3.class		ShowResultSet.java
BuildProgramMenu.java	  SequenceList$4.class		ShowSavedResults.java
ColumnData.class	  SequenceList$5.class		SplashThread.class
DragJTable.class	  SequenceList$6.class		SplashThread.java
filetree		  SequenceList$7.class		startup
form			  SequenceList.class		SwingWorker.java
ImageIconJPanel.java	  SequenceList.java
LaunchJalView.java	  SequenceListTableModel.class

jemboss/gui/filetree:
DragTree$1.class	      LocalAndRemoteFileTreeFrame$1.class
DragTree$2.class	      LocalAndRemoteFileTreeFrame$2.class
DragTree$3.class	      LocalAndRemoteFileTreeFrame$3.class
DragTree$4.class	      LocalAndRemoteFileTreeFrame$4.class
DragTree$5.class	      LocalAndRemoteFileTreeFrame$5.class
DragTree.class		      LocalAndRemoteFileTreeFrame.class
DragTree.java		      LocalAndRemoteFileTreeFrame.java
DragTree$PopupListener.class  Makefile
FileEditorDisplay.java	      Makefile.am
FileNode$1.class	      Makefile.in
FileNode.class		      RemoteDragTree.java
FileNode.java		      RemoteFileNode.java
FileSave.java		      RemoteFileTreePanel.java
FileSaving.java

jemboss/gui/form:
AlignFormat.java	   Makefile.am		    SetInFileCard.java
ApplicationNamePanel.java  Makefile.in		    SetOutFileCard.java
BuildJembossForm.java	   MultiLineToolTipUI.java  TextFieldFloat.java
JembossComboPopup.java	   PlafMacros.java	    TextFieldInt.java
LabelTextBox.java	   ReportFormat.java	    TextFieldSink.java
ListFilePanel.java	   SectionPanel.java
Makefile		   Separator.java

jemboss/gui/sequenceChooser:
CutNPasteTextArea.java	      Makefile	   OutputSequenceAttributes.java
FileChooser.java	      Makefile.am  SequenceFilter.java
InputSequenceAttributes.java  Makefile.in  TextAreaSink.java

jemboss/gui/startup:
Database.java  Makefile  Makefile.am  Makefile.in  ProgList.java

jemboss/parser:
acd			 AcdVarResolve.java  AjaxUtil.java   Makefile.am
AcdFunResolve.java	 Ajax.class	     Dependent.java  Makefile.in
AcdVariableResolve.java  Ajax.java	     Makefile	     ParseAcd.java

jemboss/parser/acd:
ApplicationFields.java	Makefile     Makefile.in
ApplicationParam.java	Makefile.am

jemboss/programs:
BatchUpdateTimer.java  ResultList.java
JembossProcess.class   ResultsUpdateTimer.java
JembossProcess.java    RunEmbossApplication2.class
ListFile.java	       RunEmbossApplication2.java
Makefile	       RunEmbossApplication2$StderrHandler.class
Makefile.am	       RunEmbossApplication2$StdoutHandler.class
Makefile.in	       RunEmbossApplication.java

jemboss/server:
AppendToLogFileThread.java  JembossServer$3.class  JembossThread.java
JembossAuthServer.java	    JembossServer$4.class  Makefile
JembossFileAuthServer.java  JembossServer$5.class  Makefile.am
JembossFileServer.java	    JembossServer.class    Makefile.in
JembossServer$1.class	    JembossServer.java	   TestPrivateServer.java
JembossServer$2.class	    JembossThread.class    TestPublicServer.java

jemboss/soap:
AuthPopup$1.class  GetACD.java		       PendingResults$2.class
AuthPopup$2.class  GetHelp.java		       PendingResults.class
AuthPopup$3.class  GetWossname.java	       PendingResults.java
AuthPopup$4.class  JembossRun.java	       PrivateRequest.java
AuthPopup$5.class  JembossSoapException.class  PublicRequest.java
AuthPopup$6.class  JembossSoapException.java   ServerSetup$1.class
AuthPopup.class    Makefile		       ServerSetup$2.class
AuthPopup.java	   Makefile.am		       ServerSetup$3.class
CallAjax.java	   Makefile.in		       ServerSetup.class
FileList.java	   MakeFileSafe.java	       ServerSetup.java
FileRoots.java	   PendingResults$1.class      ShowDB.java


Any ideas of what is going wrong?  Is the j2sdk1.3.1 the wrong version to 
use?

Regards

Pierre


--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
Personalise your mobile chart ringtones and polyphonics. Go to  
http://ringtones.com.au/ninemsn/control?page=/ninemsn/main.jsp



From ReduceBodyFat at santagifts01.com  Thu Mar 25 03:45:45 2004
From: ReduceBodyFat at santagifts01.com (Reduce Body Fat)
Date: Thu, 25 Mar 2004 06:45:45 +0300
Subject: [EMBOSS] Lower Blood Pressure and Improve Cholesterol Profile
Message-ID: <idg077Bidgfi1A0ut@santagifts01.com>

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From pscotney at hotmail.com  Thu Mar 25 07:13:37 2004
From: pscotney at hotmail.com (Pierre Scotney)
Date: Thu, 25 Mar 2004 18:13:37 +1100
Subject: [EMBOSS] Negotiating a proxy server
Message-ID: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>


Hello,

I have installed EMBOSS-2.8.0 and using the CLI (while I try to get Jemboss 
to work).  I am trying to configure the emboss.defaults file so that I can 
access the EMBL and UNIPROT SRS databases at the www.ebi.ac.uk site.  I have 
read the Administrators guide and I am unsure if I should use SRSWWW or URL 
methods for access.  I have set the entry in emboss.default to:

DB embl [ type: N method: srswww format: embl release: EBI
   dbalias: embl
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "EMBL from EBI"
   ]

DB uniprot [ type: P method: srswww format: swiss release: EBI
   dbalias: uniprot
   url: "http://srs.ebi.ac.uk/cgi-bin/wgetz"
   comment: "UNIPROT from EBI"
   ]

but then I try

$ seqret -sequence embl:AL627275 -outseq embl_AL627275
Reads and writes (returns) sequences
Error: Unable to read sequence 'embl:AL627275'
Died: seqret terminated: Bad value for '-sequence' and no prompt

This problem is compounded by the fact that I have to access the internet 
via a proxy server which I have SET emboss_proxy "myproxyserver:8080" in the 
emboss.default file.  The problem is the proxy server normally requires a 
username and password (which works for the Galeon browser).  Who can I get 
EMBOSS to issue a username and password to the proxy server for 
authentification?

I apologise for so many questions.

Regards

--
Dr Pierre Scotney
Melbourne
Australia

_________________________________________________________________
Personalise your mobile chart ringtones and polyphonics. Go to  
http://ringtones.com.au/ninemsn/control?page=/ninemsn/main.jsp



From pmr at ebi.ac.uk  Thu Mar 25 09:46:11 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Thu, 25 Mar 2004 09:46:11 +0000
Subject: [EMBOSS] Negotiating a proxy server
In-Reply-To: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>
References: <Sea2-F25Is6f3ecxddG0001bb3b@hotmail.com>
Message-ID: <4062AA63.6030607@ebi.ac.uk>

Dear Pierre

Pierre Scotney wrote:
> This problem is compounded by the fact that I have to access the 
> internet via a proxy server which I have SET emboss_proxy 
> "myproxyserver:8080" in the emboss.default file.  The problem is the 
> proxy server normally requires a username and password (which works for 
> the Galeon browser).  Who can I get EMBOSS to issue a username and 
> password to the proxy server for authentification?

Sorry, that is not yet in EMBOSS. We do know how to do it, but there has 
been very little demand so it was not implemented. I will try to test it 
and send you an update to try.

regards,

Peter Rice



From areagp61 at yahoo.it  Thu Mar 25 14:17:31 2004
From: areagp61 at yahoo.it (=?iso-8859-1?q?Graziano=20Pappad=E0?=)
Date: Thu, 25 Mar 2004 15:17:31 +0100 (CET)
Subject: [EMBOSS] software to design and execute workflows
Message-ID: <20040325141731.70168.qmail@web21001.mail.yahoo.com>

I would make aware the EMBOSS community about two new
available pieces of software that allow their users to
design and execute complex bioinformatic analysis
processes. They are interesting since these
prototypes, whose names are BioWBI (Bioinformatic
Workflow Builder Interface) and WsBAW (Web services
for Bioinformatic Analysis Workflow) at present wrap a
considerable number (about 40) of EMBOSS algorithms,
besides other algorithms that do not belong to this
package.
These prototypes are made recently available for trial
under alphaworks (http://www.alpaworks.ibm.com).


Regards

Graziano

______________________________________________________________________
Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam
http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/


From areagp61 at yahoo.it  Thu Mar 25 14:54:10 2004
From: areagp61 at yahoo.it (=?iso-8859-1?q?Graziano=20Pappad=E0?=)
Date: Thu, 25 Mar 2004 15:54:10 +0100 (CET)
Subject: [EMBOSS] software to design and execute workflows
Message-ID: <20040325145410.28826.qmail@web21007.mail.yahoo.com>

Hi all,
I have made a mistake in reporting the URL where the
prototypes are available.
The correct link is:
http://www.alphaworks.ibm.com

Regards
Graziano



______________________________________________________________________
Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam
http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/


From gbottu at ben.vub.ac.be  Thu Mar 25 16:59:52 2004
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 25 Mar 2004 17:59:52 +0100
Subject: [EMBOSS] question about databank access methods
Message-ID: <20040325165952.GC24102@bigben.ulb.ac.be>

	Dear colleagues,

I am currently using EMBOSS version 2.8.0. The manual at 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Admin_guide/
adminguide/node4.html#SECTION00421000000000000000
mentions for the databank access method "DIRECT"

DB mydb [ 
#required parameters
   method: "direct"
   format: "embl"
   type: "N"
   dir: "\$emboss_db_dir/mydb"
   file: "*.dat"   
#optional parameters
   fields: "sv des key org"
   release: "63.0"
   comment: "My own database with no indices"
   exclude: "est*.dat"
]

I tried the "exclude" parameter and it did not work. Do I miss something ?
Has someone already used it successfully ?

	Guy Bottu,
	Belgian EMBnet Node


From stefanielager at fastmail.ca  Fri Mar 26 07:45:26 2004
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Fri, 26 Mar 2004 07:45:26 +0000 (UTC)
Subject: [EMBOSS] Negotiating a proxy server
Message-ID: <20040326074527.A40F18640CB@mail.interchange.ca>

If it's possible to define domains which you don't want to use proxy for
(as you can do in Mozilla and other web-browsers), that would be nice.
Otherwise you have to use ONLY internal databases or ONLY external
databases, since you often can't go though proxy for internal web pages.

Stefanie

> Dear Pierre
> 
> Pierre Scotney wrote:
>> This problem is compounded by the fact that I have to access the
>> internet via a proxy server which I have SET emboss_proxy
>> "myproxyserver:8080" in the emboss.default file.  The problem is the
>> proxy server normally requires a username and password (which works
>> for the Galeon browser).  Who can I get EMBOSS to issue a username
>> and password to the proxy server for authentification?
> 
> Sorry, that is not yet in EMBOSS. We do know how to do it, but there
> has been very little demand so it was not implemented. I will try to
> test it and send you an update to try.
> 
> regards,
> 
> Peter Rice
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians


From fnovo at unav.es  Fri Mar 26 09:22:56 2004
From: fnovo at unav.es (F.J. Novo)
Date: Fri, 26 Mar 2004 10:22:56 +0100
Subject: [EMBOSS] refseq IDs via SRSWWW
Message-ID: <4063F670.8020100@unav.es>

Hello, I've just configured a remote access to genbank in my 2.8.0 
installation, as suggested:

DB genbank [ type: N method: srswww format: genbank release: NCBI
    comment: "Genbank from NCBI"
    url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
]

It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems 
unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?
Cheers,


-- 
Dr. Francisco J. Novo
Department of Genetics
University of Navarra
31080 Pamplona (SPAIN)
Tel + 948 425600 (ext 6252)
Fax + 948 425649
www.unav.es/genetica/



From gwilliam at hgmp.mrc.ac.uk  Fri Mar 26 09:27:42 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Fri, 26 Mar 2004 09:27:42 +0000
Subject: [EMBOSS] refseq IDs via SRSWWW
References: <4063F670.8020100@unav.es>
Message-ID: <4063F78E.47946DC9@hgmp.mrc.ac.uk>

RefSeq is a separate database to GenBank.
They are both produced by NCBI.
You will have to retrieve and install these two databases independently.

ftp://ftp.ncbi.nih.gov/genbank
ftp://ftp.ncbi.nih.gov/refseq

Gary Williams

"F.J. Novo" wrote:
> 
> Hello, I've just configured a remote access to genbank in my 2.8.0
> installation, as suggested:
> 
> DB genbank [ type: N method: srswww format: genbank release: NCBI
>     comment: "Genbank from NCBI"
>     url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
> ]
> 
> It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems
> unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?
> Cheers,
> 
> --
> Dr. Francisco J. Novo
> Department of Genetics
> University of Navarra
> 31080 Pamplona (SPAIN)
> Tel + 948 425600 (ext 6252)
> Fax + 948 425649
> www.unav.es/genetica/

-- 
Gary Williams
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494522			Fax: +44 1223 494512
E-mail: gwilliam at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From pmr at ebi.ac.uk  Fri Mar 26 09:57:12 2004
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 26 Mar 2004 09:57:12 +0000
Subject: [EMBOSS] refseq IDs via SRSWWW
In-Reply-To: <4063F670.8020100@unav.es>
References: <4063F670.8020100@unav.es>
Message-ID: <4063FE78.1030002@ebi.ac.uk>

F.J. Novo wrote:

> Hello, I've just configured a remote access to genbank in my 2.8.0 
> installation, as suggested:
> 
> DB genbank [ type: N method: srswww format: genbank release: NCBI
>    comment: "Genbank from NCBI"
>    url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
> ]
> 
> It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems 
> unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?

srswww will query by id and acc.

You can query a remote SRS database for any ID or ACC value.

If you define some extra fields, you can query by description, organism 
and keyword.

The NM_xxxxx codes are NCBI's REFSEQ identifiers. GenBank entries may 
refer to them, but they are not indexed by them.

At the Canadian SRS server, the REFSEQ DNA entries are in REFSEQNT so 
you can define that as a database (use dbalias:refseqnt in the EMBOSS db 
definition if you want to use another database name locally)

We have considered providing an Entrez access method to try retrieving 
these strange identifiers (refseq, GI numbers, and so on) from NCBI but 
(a) they change the Entrez interface each time I look and (b) it 
requires far too much rewriting of parsers each time to get to the 
actual entries. Some day, if it becomes stable and if one can query byu 
such fields and get straight to the entries then we may implement it.

Hope this helps,

Peter Rice



From Paul.Baumgartner at unibas.ch  Fri Mar 26 13:48:58 2004
From: Paul.Baumgartner at unibas.ch (Paul Baumgartner)
Date: Fri, 26 Mar 2004 14:48:58 +0100
Subject: [EMBOSS] pdb entries
Message-ID: <54DAE476-7F2C-11D8-8B31-003065B9531E@unibas.ch>

Hi

how should I define the DB pdb [ ? ? ..? ] entry in .embossrc, to 
retrieve coordinates-files from Protein Data Bank (pdb), via 'entret' 
from url: http://srs.ebi.ac.uk/cgi-bin/wgetz ?

Thanks

Biozentrum
Paul Baumgartner
Zellbiologie
Klingelbergstrasse 70
CH-4056 Basel



From pseelig at hfriedman.rdsl.lmi.net  Sat Mar 27 03:46:28 2004
From: pseelig at hfriedman.rdsl.lmi.net (doctor)
Date: Sat, 27 Mar 2004 03:46:28 +0000
Subject: [EMBOSS] imemproove your health
In-Reply-To: <H5AAGB69JAD63I7F@embnet.org>
References: <H5AAGB69JAD63I7F@embnet.org>
Message-ID: <7HG99EBB6G6EBCA5@hfriedman.rdsl.lmi.net>

Afteri the age of twenty-onen, your body slowly stopsv releasing an important hormoane known as Human Growgth Hoyrmone. 
The reduction of Human Growpth Hoermone, which regulates levels of other hosrmones in the body (including testosterogne, estrogden, progesterolne, and melatondin) is directly responsible for many of the most common signsn of growing old, such as wrinkles, gray hair, decreased energy, and diminished semxual function. 

Human Growgth Horpmone

Boost your immunen system 
Rejuvenapte your body and mind 
Feel & looka younger 
Reduce wriwnkles, lose weight, decrease cellemulite 
Restore your seex drive and vuigor 
Revitfalize your heart, liver, kidneys & lungs 
Maintain muscloe mass 
Refresh memory, mood and mentaql energy 
Sleep soundldy and awake rested 
Help eliminate stremss, fatigue and depression 2 

Read http://mybestchoice.net/hgh/index.php?pid=eph9058 for more information



From areagp61 at yahoo.it  Fri Mar 26 11:36:44 2004
From: areagp61 at yahoo.it (=?iso-8859-1?Q?Graziano_Pappad=E0?=)
Date: Fri, 26 Mar 2004 12:36:44 +0100
Subject: [EMBOSS] software to design and execute workflows wrong download link
Message-ID: <003d01c41326$a035c560$18105709@JTCDOMAIN>

Hi all,
in the following page http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html#other, it seems that the the BioWBI and WsBAW interfaces can be downloaded at ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz, but this link is wrong!
BioWBI and WsBAW can only be accessed online at the alphaworks site using the following links:

BioWBI       -->     http://www.alphaworks.ibm.com/tech/biowbi
WsBAW     -->     http://www.alphaworks.ibm.com/tech/wsbaw

Regards

Graziano

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From EliminateBugs at bargainsdaily01.com  Mon Mar 29 03:34:30 2004
From: EliminateBugs at bargainsdaily01.com (Eliminate Bugs)
Date: Mon, 29 Mar 2004 07:34:30 +0400
Subject: [EMBOSS] Complimentary Scan for your PC
Message-ID: <idg077Bidgfi1A0ut@bargainsdaily01.com>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20040329/1046b794/attachment-0001.html>

From letondal at pasteur.fr  Mon Mar 29 08:24:44 2004
From: letondal at pasteur.fr (Catherine Letondal)
Date: Mon, 29 Mar 2004 10:24:44 +0200
Subject: [EMBOSS] software to design and execute workflows wrong download link 
In-Reply-To: Your message of "Fri, 26 Mar 2004 12:36:44 +0100."
             <003d01c41326$a035c560$18105709@JTCDOMAIN> 
Message-ID: <200403290824.i2T8Oibc452617@electre.pasteur.fr>


Graziano_Pappad? wrote:
> 
> Hi all,
> in the following page =
> http://www.hgmp.mrc.ac.uk/Software/EMBOSS/interfaces.html#other, it =
> seems that the the BioWBI and WsBAW interfaces can be downloaded at =
> ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/G-Pipe.tar.gz, but this =
> link is wrong!

It's not. I have just checked it. 
(we had some Internet connection problems these days, thank you Worldcom)

> BioWBI and WsBAW can only be accessed online at the alphaworks site =
> using the following links:
> 
> BioWBI       -->     http://www.alphaworks.ibm.com/tech/biowbi
> WsBAW     -->     http://www.alphaworks.ibm.com/tech/wsbaw
> 
> Regards
> 
> Graziano
> 
> 
>

--
Catherine Letondal -- Pasteur Institute Computing Center


From ranrub at md.huji.ac.il  Mon Mar 29 15:02:12 2004
From: ranrub at md.huji.ac.il (Ran Rubinstein)
Date: Mon, 29 Mar 2004 17:02:12 +0200
Subject: [EMBOSS] Negotiating a proxy server
In-Reply-To: <20040326074527.A40F18640CB@mail.interchange.ca>
Message-ID: <006b01c4159e$d11c5ed0$7ea74084@sauron>

Pierre,

It's possible to circumvent the proxy password problem by installing a local
squid proxy on your machine (or any other machine) and having it access the
password protected proxy as a parent proxy (squid supports password
authentication).
In your emboss.default you then define the proxy as localhost:3128 or
however you installed squid.

Hope this helps,
--?
Ran Rubinstein 
Dept. of Molecular Biology 
Faculty of Medicine, Hebrew University, Ein Karem, Jerusalem, Israel
Tel +972-2-6757906 Fax +972-2-6758992


-----Original Message-----
From: owner-emboss at hgmp.mrc.ac.uk [mailto:owner-emboss at hgmp.mrc.ac.uk] On
Behalf Of Stefanie Lager
Sent: Friday, March 26, 2004 9:45 AM
To: emboss at embnet.org
Subject: Re: [EMBOSS] Negotiating a proxy server

If it's possible to define domains which you don't want to use proxy for
(as you can do in Mozilla and other web-browsers), that would be nice.
Otherwise you have to use ONLY internal databases or ONLY external
databases, since you often can't go though proxy for internal web pages.

Stefanie

> Dear Pierre
> 
> Pierre Scotney wrote:
>> This problem is compounded by the fact that I have to access the
>> internet via a proxy server which I have SET emboss_proxy
>> "myproxyserver:8080" in the emboss.default file.  The problem is the
>> proxy server normally requires a username and password (which works
>> for the Galeon browser).  Who can I get EMBOSS to issue a username
>> and password to the proxy server for authentification?
> 
> Sorry, that is not yet in EMBOSS. We do know how to do it, but there
> has been very little demand so it was not implemented. I will try to
> test it and send you an update to try.
> 
> regards,
> 
> Peter Rice
_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



From jison at hgmp.mrc.ac.uk  Mon Mar 29 19:08:00 2004
From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison)
Date: Mon, 29 Mar 2004 20:08:00 +0100
Subject: [EMBOSS] pdb entries
References: <54DAE476-7F2C-11D8-8B31-003065B9531E@unibas.ch>
Message-ID: <40687410.57D9C187@hgmp.mrc.ac.uk>

Hi Paul

PDB is not (yet) fully supported under EMBOSS.

There are functions to parse PDB files and applications
to do the same and generate "clean" files of coordinate
and derived data, but PDB format is not (yet) suported
in the way I think you envisage using it.

Let me know what you want to do with PDB and why and
I'll see if EMBOSS can (be made to) do it.

Cheers

Jon


Paul Baumgartner wrote:

> Hi
>
> how should I define the DB pdb [ ? ? ..? ] entry in .embossrc, to
> retrieve coordinates-files from Protein Data Bank (pdb), via 'entret'
> from url: http://srs.ebi.ac.uk/cgi-bin/wgetz ?
>
> Thanks
>
> Biozentrum
> Paul Baumgartner
> Zellbiologie
> Klingelbergstrasse 70
> CH-4056 Basel

--
Jon C. Ison, PhD
Proteomics Applications Group
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Tel: +44 1223 494500  Fax: +44 1223 494512
E-mail: jison at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk