From henrikki.almusa at helsinki.fi  Mon Dec  1 06:54:49 2003
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Mon, 1 Dec 2003 13:54:49 +0200
Subject: [EMBOSS] EMBOSS 2.8.0 released
In-Reply-To: <200311301704.hAUH4tei000865@bromine.hgmp.mrc.ac.uk>
References: <200311301704.hAUH4tei000865@bromine.hgmp.mrc.ac.uk>
Message-ID: <200312011354.49516.henrikki.almusa@helsinki.fi>

On Sunday 30 November 2003 19:04, Alan Bleasby wrote:
> EMBOSS 2.8.0 is available for download from:
>
>   http://www.uk.embnet.org/Software/EMBOSS
>   ftp://ftp.uk.embnet.org/pub/EMBOSS
>
<snip>
>
> EMBASSY
>
> Note that, because of the ACD changes mentioned above, those sites who
> install the EMBASSY packages (also in ftp://ftp.uk.embnet.org/pub/EMBOSS/)
> will need to re-ftp and build them.

Is there any info on whether (and if so, when)  the newer version of phylip 
(3.6) is going to be embassified? In given directory there is only the older 
version (3.57c).

Thanks,
-- 
Henrikki Almusa


From chalaouxfr at wanadoo.fr  Tue Dec  2 06:55:26 2003
From: chalaouxfr at wanadoo.fr (fr chalaoux)
Date: Tue, 2 Dec 2003 12:55:26 +0100
Subject: [EMBOSS] cirdna problem on macosx
Message-ID: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>

Hi all,

As noted in  
http://www.mail-archive.com/fink-devel at lists.sourceforge.net/ 
msg06607.html , I confirm the problem.

It even subsists in EMBOSS 2.8.0 ...

Simon



From pmr at ebi.ac.uk  Tue Dec  2 07:06:37 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 02 Dec 2003 12:06:37 +0000
Subject: [EMBOSS] cirdna problem on macosx
In-Reply-To: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>
References: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>
Message-ID: <3FCC804D.30609@ebi.ac.uk>

fr chalaoux wrote:

> Hi all,
> 
> As noted in  
> http://www.mail-archive.com/fink-devel at lists.sourceforge.net/ 
> msg06607.html , I confirm the problem.
> 
> It even subsists in EMBOSS 2.8.0 ...

cirdna and lindna have some fixed array sizes which need fixing for some 
systems (and, as it happens, for valgrind memory tests).

Non-urgent (cirdna and lindna are not, as faras I am aware, highly 
used), so to be fixed in a future release... but quite soon.

As a quick fix, you can reduce MAXLABELS and perhaps MAXGROUPS in 
cirdna.c and lindna.c

Hope that helps,

Peter Rice




From kvddrift at earthlink.net  Tue Dec  2 17:19:30 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Tue, 2 Dec 2003 17:19:30 -0500
Subject: [EMBOSS] cirdna problem on macosx
In-Reply-To: <3FCC804D.30609@ebi.ac.uk>
References: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr> <3FCC804D.30609@ebi.ac.uk>
Message-ID: <992CCEDC-2515-11D8-B643-003065A5FDCC@earthlink.net>


On Dec 2, 2003, at 7:06 AM, Peter Rice wrote:

> cirdna and lindna have some fixed array sizes which need fixing for 
> some systems (and, as it happens, for valgrind memory tests).
>
> Non-urgent (cirdna and lindna are not, as faras I am aware, highly 
> used), so to be fixed in a future release... but quite soon.
>
> As a quick fix, you can reduce MAXLABELS and perhaps MAXGROUPS in 
> cirdna.c and lindna.c
>


I am the maintainer of EMBOSS for fink. I have patched EMBOSS for fink 
that solves the above problem. Let me know if you want the updated info 
and patch file (for EMBOSS 2.8.0). I will submit them to fink, and 
hopefully they will be available in the tree asap.

- Koen.



From stefanielager at fastmail.ca  Wed Dec  3 02:17:18 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 3 Dec 2003 02:17:18 -0500 (EST)
Subject: [EMBOSS] siRNA improvements 
Message-ID: <3FCD8DFE.000201.00920@ns.interchange.ca>

Hi,

It would be nice if the EMBOSS application sirna could incorporate
simple calculation of free energy, to improve the siRNA design. Lately
several reports on siRNA design (reviewed in Silva et al 2003) have
showed the importance of making the 5' end of the antisense strand
less stable than the 3' end (Schwarz et al 2003). Also the center part
should show a lower internal stability (Khvorova et al 2003). Simple
energy profiles can be calculated by the method of Mathews et al
(Mathews et al 1999). Several of the commercial siRNA design servers
have already incorporated free energy parameters in the design, and it
would really be nice to have an alternative.

Stefanie


Silva JM, Sachidanandam R, Hannon GJ.
Free energy lights the path toward more effective RNAi  
Nat. Genet. 2003, 35:303-305.

Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. 
Asymmetry in the assembly of the RNAi enzyme complex.
Cell. 2003 115:199-208.

Khvorova A, Reynolds A, Jayasena SD. 
Functional siRNAs and miRNAs exhibit strand bias.
Cell. 2003 115:209-216.

Mathews DH, Sabina J, Zuker M, Turner DH. 
Expanded sequence dependence of thermodynamic parameters improves
prediction of RNA secondary structure.
J Mol Biol. 1999 288:911-940.


_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From henrikki.almusa at helsinki.fi  Wed Dec  3 04:12:09 2003
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Wed, 3 Dec 2003 11:12:09 +0200
Subject: [EMBOSS] Jemboss dan+emma
Message-ID: <200312031112.09865.henrikki.almusa@helsinki.fi>

Hello,

I'm currently using emboss 2.8.0 and also jemboss as stand-alone client. I 
have problem with Dan and Emma. 

Dan. It can be run, but no output was produced. The window (view result) is 
empty and if I try to save trace is produced.

Emma. If run without pressing "load sequence attributes" it also will have 
empty result. Pressing the button will produce the trace.

Both of these work on commandline without problems. Both traces are in same 
file.

Thanks,
-- 
Henrikki Almusa
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From ame at esbs.u-strasbg.fr  Wed Dec  3 04:45:56 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Wed, 3 Dec 2003 10:45:56 +0100
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <7E4502ED-2575-11D8-AE7F-0005024329A7@esbs.u-strasbg.fr>

Hello,

I am writing for a request for emboss. It would be great that emboss 
could integrate something similar to the very useful (my point of view) 
GCG's program MAPPLOT (a graphical representation of a restriction 
map). I am sure that could be easily added to emboss's remap or 
restrict.
With this feature added I would definitively not use anymore GCG.
Any idea. Thanks for the great job.
Jean-Christophe

________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From gwilliam at hgmp.mrc.ac.uk  Wed Dec  3 04:49:06 2003
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 03 Dec 2003 09:49:06 +0000
Subject: [EMBOSS] siRNA improvements
References: <3FCD8DFE.000201.00920@ns.interchange.ca>
Message-ID: <3FCDB192.62A98DC8@hgmp.mrc.ac.uk>

Thanks for the suggestions.
I'll take a look.
Gary

Stefanie Lager wrote:
> 
> Hi,
> 
> It would be nice if the EMBOSS application sirna could incorporate
> simple calculation of free energy, to improve the siRNA design. Lately
> several reports on siRNA design (reviewed in Silva et al 2003) have
> showed the importance of making the 5' end of the antisense strand
> less stable than the 3' end (Schwarz et al 2003). Also the center part
> should show a lower internal stability (Khvorova et al 2003). Simple
> energy profiles can be calculated by the method of Mathews et al
> (Mathews et al 1999). Several of the commercial siRNA design servers
> have already incorporated free energy parameters in the design, and it
> would really be nice to have an alternative.
> 
> Stefanie
> 
> Silva JM, Sachidanandam R, Hannon GJ.
> Free energy lights the path toward more effective RNAi
> Nat. Genet. 2003, 35:303-305.
> 
> Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD.
> Asymmetry in the assembly of the RNAi enzyme complex.
> Cell. 2003 115:199-208.
> 
> Khvorova A, Reynolds A, Jayasena SD.
> Functional siRNAs and miRNAs exhibit strand bias.
> Cell. 2003 115:209-216.
> 
> Mathews DH, Sabina J, Zuker M, Turner DH.
> Expanded sequence dependence of thermodynamic parameters improves
> prediction of RNA secondary structure.
> J Mol Biol. 1999 288:911-940.
> 
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians

-- 
Gary Williams	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: name at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From shrish at ccmb.res.in  Wed Dec  3 04:04:45 2003
From: shrish at ccmb.res.in (Shrish Tiwari)
Date: Wed, 3 Dec 2003 14:34:45 +0530
Subject: [EMBOSS] MFOLD
Message-ID: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>

Hi!

Is it possible to include MFOLD, for computing DNA/RNA folds into EMBOSS?

Shrish


______________________________________________________________________
Dr. Shrish Tiwari
BIC, Centre for Cellular and Molecular Biology
Uppal Road, Hyderabad - 500 007
Phone: 91-40-7192776 (work), 91-40-7156603 (home)
email: shrish at ccmb.res.in
______________________________________________________________________



From stefanielager at fastmail.ca  Wed Dec  3 08:08:30 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 3 Dec 2003 08:08:30 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCDE04E.000011.77674@ns.interchange.ca>

The program TACG ( http://tacg.sourceforge.net/) can substitute for
some of the GCG applications missing in EMBOSS. Like 

mapplot (tacg -l -s )
map (tacg -T3,1 -sL )
mapsort (tacg -cF2 )
mapgel (tacg -g10 -s )
findpatterns (tacg -S2 -R 'path/to/a/pattern/file )

Stefanie

> Hello,
> 
> I am writing for a request for emboss. It would be great that
> emboss could integrate something similar to the very useful (my
> point of view) GCG's program MAPPLOT (a graphical representation
> of a restriction map). I am sure that could be easily added to
> emboss's remap or restrict.
> With this feature added I would definitively not use anymore GCG.
> Any idea. Thanks for the great job.
> Jean-Christophe
> 
> ________________________
> Jean-Christophe Am?, PhD
> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
> Structurale
> ?cole Sup?rieure de Biotechnologie de Strasbourg
> P?le API
> Parc d'innovation, Boulevard S?bastien Brant
> BP 10413
> 67412 ILLKIRCH CEDEX
> France
> 
> tel.: 33 3 90 24 47 05
> Fax.: 33 3 90 24 46 86

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From gilal at md.huji.ac.il  Wed Dec  3 09:47:51 2003
From: gilal at md.huji.ac.il (Gila Lithwick)
Date: Wed, 03 Dec 2003 16:47:51 +0200
Subject: [EMBOSS] water problems
Message-ID: <3FCDF797.8020309@md.huji.ac.il>

Hello,

I wasn't sure which mailing list this e-mail is more appropriate for, so 
I've sent it to both...

I have been using EMBOSS, and noticed the following problems with water:

1) Water does not give a gap extension penalty for the first gap.  This 
is not how gaps are generally penalized.
For example, the alignment between tttttcccaaaaa and tttttaaaaa is:
seq1               1 tttttcccaaaaa     13
                     |||||   |||||
seq2               1 ttttt---aaaaa     10
EMBOSS scores this 39, however the score should be 10*5-3*0.5-10=38.5
Is this correct?

2) Since the default gap extension penalty is so low (0.5), water often 
gives very long alignments.  A slightly higher gap penalty (for example 
1) gives better alignments - maybe it would be better to make this the 
default.

3) It would be very useful if there was a way to assess significance of 
pairwise alignments, such as the -rand option in gcg.  It is possible, 
of course, to do each step (shuffling one sequence, aligning, and 
calculating the mean and standard deviation) separately.  However, for 
users that don't know how to program, this isn't simple.

Thank you,
Gila.



From lmullan at hgmp.mrc.ac.uk  Wed Dec  3 09:56:10 2003
From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan)
Date: Wed, 3 Dec 2003 14:56:10 +0000 (GMT)
Subject: [EMBOSS] Re: [EMBOSS-BUG] water problems
In-Reply-To: <3FCDF797.8020309@md.huji.ac.il>
Message-ID: <Pine.SOL.4.44.0312031453520.3443-100000@bromine>

Hi!

EMBOSS is scorring it correctly. You have three gaps in thie alignment.
The first gap incurs a penalty of ten for opeing the gap. And then the
subsequent gaps incur penalties of 0.5 each therefore the calculation is:

(10*5)-10-(2*0.5) = 39

I think you got over zealous with your extensions!!

Lisa

Lisa Mullan
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: lmullan at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk

On Wed, 3 Dec 2003, Gila Lithwick wrote:

> Hello,
>
> I wasn't sure which mailing list this e-mail is more appropriate for, so
> I've sent it to both...
>
> I have been using EMBOSS, and noticed the following problems with water:
>
> 1) Water does not give a gap extension penalty for the first gap.  This
> is not how gaps are generally penalized.
> For example, the alignment between tttttcccaaaaa and tttttaaaaa is:
> seq1               1 tttttcccaaaaa     13
>                      |||||   |||||
> seq2               1 ttttt---aaaaa     10
> EMBOSS scores this 39, however the score should be 10*5-3*0.5-10=38.5
> Is this correct?
>
> 2) Since the default gap extension penalty is so low (0.5), water often
> gives very long alignments.  A slightly higher gap penalty (for example
> 1) gives better alignments - maybe it would be better to make this the
> default.
>
> 3) It would be very useful if there was a way to assess significance of
> pairwise alignments, such as the -rand option in gcg.  It is possible,
> of course, to do each step (shuffling one sequence, aligning, and
> calculating the mean and standard deviation) separately.  However, for
> users that don't know how to program, this isn't simple.
>
> Thank you,
> Gila.
>



From ame at esbs.u-strasbg.fr  Wed Dec  3 10:22:07 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Wed, 3 Dec 2003 16:22:07 +0100
Subject: [EMBOSS] remap and GCG mapplot
In-Reply-To: <3FCDE04E.000011.77674@ns.interchange.ca>
References: <3FCDE04E.000011.77674@ns.interchange.ca>
Message-ID: <74EAFDAC-25A4-11D8-AE7F-0005024329A7@esbs.u-strasbg.fr>

It looks good, but I tried to compiled it with MacOSX 10.3 and I got a 
lot of errors...

Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :

> The program TACG ( http://tacg.sourceforge.net/) can substitute for
> some of the GCG applications missing in EMBOSS. Like
>
> mapplot (tacg -l -s )
> map (tacg -T3,1 -sL )
> mapsort (tacg -cF2 )
> mapgel (tacg -g10 -s )
> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>
> Stefanie
>
>> Hello,
>>
>> I am writing for a request for emboss. It would be great that
>> emboss could integrate something similar to the very useful (my
>> point of view) GCG's program MAPPLOT (a graphical representation
>> of a restriction map). I am sure that could be easily added to
>> emboss's remap or restrict.
>> With this feature added I would definitively not use anymore GCG.
>> Any idea. Thanks for the great job.
>> Jean-Christophe
>>
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>>
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
>
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From mad at biol.unlp.edu.ar  Wed Dec  3 19:01:19 2003
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?B?TWFydO1uIFNhcmFjaHU=?=)
Date: Wed,  3 Dec 2003 21:01:19 -0300
Subject: [EMBOSS] MFOLD
In-Reply-To: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>
References: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>
Message-ID: <1070496079.3fce794f04abb@www.biol.unlp.edu.ar>

At BEN (Belgian EMBnet Node) they are developing a wrapper to use mfold within 
EMBOSS, but I don't know if it is ready for distribution.

Regards,

martin

Quoting Shrish Tiwari <shrish at ccmb.res.in>:

> Hi!
> 
> Is it possible to include MFOLD, for computing DNA/RNA folds into EMBOSS?
> 
> Shrish
> 
> 
> ______________________________________________________________________
> Dr. Shrish Tiwari
> BIC, Centre for Cellular and Molecular Biology
> Uppal Road, Hyderabad - 500 007
> Phone: 91-40-7192776 (work), 91-40-7156603 (home)
> email: shrish at ccmb.res.in
> ______________________________________________________________________
> 


-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org


From stefanielager at fastmail.ca  Thu Dec  4 01:17:43 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 4 Dec 2003 01:17:43 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCED187.00006F.07204@ns.interchange.ca>

I don't know anything about MacOSX, but when I had problems with TACG
on Linux Harry Mangalam sent me the latest TACG version 4.0, which
solved my compilation problems.

Stefanie

> It looks good, but I tried to compiled it with MacOSX 10.3 and I
> got a lot of errors...
> 
> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
> 
>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>> for some of the GCG applications missing in EMBOSS. Like
>> 
>> mapplot (tacg -l -s )
>> map (tacg -T3,1 -sL )
>> mapsort (tacg -cF2 )
>> mapgel (tacg -g10 -s )
>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>> 
>> Stefanie
>> 
>>> Hello,
>>> 
>>> I am writing for a request for emboss. It would be great that
>>> emboss could integrate something similar to the very useful (my
>>> point of view) GCG's program MAPPLOT (a graphical representation
>>> of a restriction map). I am sure that could be easily added to
>>> emboss's remap or restrict.
>>> With this feature added I would definitively not use anymore
>>> GCG. Any idea. Thanks for the great job.
>>> Jean-Christophe
>>> 
>>> ________________________
>>> Jean-Christophe Am?, PhD
>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>>> Structurale
>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>> P?le API
>>> Parc d'innovation, Boulevard S?bastien Brant
>>> BP 10413
>>> 67412 ILLKIRCH CEDEX
>>> France
>>> 
>>> tel.: 33 3 90 24 47 05
>>> Fax.: 33 3 90 24 46 86
>> 
>> _________________________________________________________________
>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
> ________________________
> Jean-Christophe Am?, PhD
> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
> Structurale
> ?cole Sup?rieure de Biotechnologie de Strasbourg
> P?le API
> Parc d'innovation, Boulevard S?bastien Brant
> BP 10413
> 67412 ILLKIRCH CEDEX
> France
> 
> tel.: 33 3 90 24 47 05
> Fax.: 33 3 90 24 46 86

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From stefanielager at fastmail.ca  Thu Dec  4 05:25:14 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 4 Dec 2003 05:25:14 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCF0B8A.0000F7.07220@ns.interchange.ca>

The "Changelog" of TACG 4.0 says that it has been built on Solaris 5.8
(gcc) and on Mac OSX 10.2 .

Stefanie

"Change Log for tacg development

$Id: ChangeLog,v 1.1.1.1 2001/11/14 18:36:33 mangalam Exp $ 

2003.05.30 Harry Mangalam, hjm at tacgi.com 
 * fixed the ghostscript bug - still some problems in the generation
of the 
   postscript - not enuf error checking, but the thang executes as
it's supposed 
   toat least if the postscript is good.

2003.05.29 Harry Mangalam, hjm at tacgi.com 
 * minor fix to seqio.c to allow OSX to include <dirent.h>
 * removed fmax() declaration - there was no parallel function anyway - 
   looked like the floating point match to imax() but no code for it.
 * Fixed a bunch of stuff in the configure /make process so things don't 
   break on different platforms
 * updated the config.guess & config.sub to allow finding OSX
 * re-included getopt1.c so that it compiles on Solaris - otherwise 
   getopt_long doesn't get defined.
 * added the psprolog file to the tarball so --ps, --pdf can work.
 * added automatic making of newdist and tarball to automagically
build a distro -
   this now works very well and keeps track of the key files to include.
 * tested build procedure on sf compile farm on the following machines:
 
   - Debian 2.2 Intel SMP (gcc 2.95)
     Linux usf-cf-x86-linux-1 2.4.19 #1 SMP  i686 unknown
   
   - RedHat 7.3 Intel SMP (gcc 2.96)
     Linux usf-cf-x86-linux-2.cf.sourceforge.net 2.4.18-5smp #1 SMP \
     i686 unknown
   
   - Debian 3.0  Alpha (gcc 2.95.4)
     Linux usf-cf-alpha-linux-1 2.2.20 #2 alpha unknown
     
   - Debian SPARC (gcc 2.95)
     Linux usf-cf-sparc-linux-1 2.4.18 #2  sparc64 unknown
     
   - Solaris 5.8 (gcc )
      
   - Mac OSX 10.2 (gcc 3.1)
     Darwin ucf-cf-ppc-macosx-2 6.5 Darwin Kernel Version 6.5:  \
     root:xnu/xnu-344.32.obj~1/RELEASE_PPC  Power Macintosh powerpc
   

2003.05.19 Harry Mangalam, hjm at tacgi.com 
 * changed --idonly to have default as 1 (don't have to specify the
flag value)
 

2003.05.16 Harry Mangalam, hjm at tacgi.com 
 * tested vs the old readseq test sequences - seems to read all but
   test.m-paup and test.strider (ascii format).  Have to verify a 
   bit more and see what' not working.  Since I have the binary 
   strider format reader working - it might be useful to mod seqio 
   to do that as well using pcre.
 * fixed a BUG that filtered teh wrong enzyme (filtered on proto 
   index instead of proto[index])
 * added and cleaned up verbosity levels so that verbosity is 
   upwardly inclusive (ie -V3 contains all the verbosity of V1 and V2)
 * make install, make newdist, make tarball, make install_web added to
   Makefile.in and they seem to work altho install_web just tells the 
   user what to do - edit & run the web installer script.

2003.05.09 Harry Mangalam, hjm at tacgi.com 
 * removed all traces of udping.c and udp reporting from code.
 
2003.03.14 Harry Mangalam, hjm at tacgi.com  
 * RE contains .E_olap which is the size of the overlap,
   if any.  Could  be combined with -o to provide selection of REs
   that provide only 5' overhangs  of size 3, for example. currently
   -o5, -o0 -o3; could graft on a hack to allow  user to extend to
   add a number if 5 or 3 ie -o5,5 which would select only REs  that
   have a 5' overhang of length 5 - OK!  Done!


2003.02.25.23 Harry Mangalam, hjm at tacgi.com 
 * 2.25.03 - Brian Frist sez following work on both Linux and SOlaris:
   Fasta EMBL Genbank IG Plain NBRF Phylip3.2 Phylip MSF but there are
some 
   others that fail mysteriously on some platforms - not completely
solved yet..
 * Following worked on Linux but not on SOlaris:
   Phylip3.2 Phylip MSF

 * Following worked on Solaris but not on Linux:
   CODATA

 * and NONE of the other formats generated by readseq worked on either, 
   not even GCG
   This disagrees with running the test sequences from readseq thru it
tho..
   requires more investigation...

   
2002-11.23 Harry Mangalam, hjm at tacgi.com 
  * added code to add a '-' to site numbers when nonpals are found on the
    bottom strand (suggested by Stefanie Lager), so that Site output now
    includes both positive and negative numbers (all numbered relative
to the
    top strand tho).  Still need to add a mod to -S flag to optionally
enable 
    this, tho.
  * added and modified code to allow pattern labels longer than 10
chars - 
    now have to be #defined for building in tacg.h (MAX_PAT_NAME_LEN) and 
    then the RE struct is checked for the longest name and that length is 
    used for output, etc (stored in F.MaxPatNameLen).

2001-10-17 Harry Mangalam, hjm at tacgi.com 
   * Fixed BAD realloc bug in ReadEnz in which test for end of
alloc'ed mem in
      RE was  calculated wrong - basic math error.  Showed up bc
trying to do a
      bunch of matching with errors and the cal overflowed the end of RE.

2001-06-09 Harry Mangalam, hjm at tacgi.com  
  * Added & deleted a bunch of files from CVS to bring things up to date
  * made the Logging of Degens optional to save memory
  * brought tacg.1 man page more up to date.
  * "

> I had no success on Solaris and FreeBSD.
> So on what system should the version 3.5 compile ?
> Do you have any information from the author why the current
> version 4 is not available from sourceforge ?
> 
> Cheers,
> David.
> 
> 
> I don't know anything about MacOSX, but when I had problems with
> TACG on Linux Harry Mangalam sent me the latest TACG version 4.0,
> which solved my compilation problems.
> 
> Stefanie
> 
>> It looks good, but I tried to compiled it with MacOSX 10.3 and I
>> got a lot of errors...
>> 
>> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
>> 
>>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>>> for some of the GCG applications missing in EMBOSS. Like
>>> 
>>> mapplot (tacg -l -s )
>>> map (tacg -T3,1 -sL )
>>> mapsort (tacg -cF2 )
>>> mapgel (tacg -g10 -s )
>>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>>> 
>>> Stefanie
>>> 
>>>> Hello,
>>>> 
>>>> I am writing for a request for emboss. It would be great that
>>>> emboss could integrate something similar to the very useful (my
>>>> point of view) GCG's program MAPPLOT (a graphical
>>>> representation of a restriction map). I am sure that could be
>>>> easily added to emboss's remap or restrict.
>>>> With this feature added I would definitively not use anymore
>>>> GCG. Any idea. Thanks for the great job.
>>>> Jean-Christophe
>>>> 
>>>> ________________________
>>>> Jean-Christophe Am?, PhD
>>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire
>>>> et Structurale
>>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>>> P?le API
>>>> Parc d'innovation, Boulevard S?bastien Brant
>>>> BP 10413
>>>> 67412 ILLKIRCH CEDEX
>>>> France
>>>> 
>>>> tel.: 33 3 90 24 47 05
>>>> Fax.: 33 3 90 24 46 86
>>> 
>>> ________________________________________________________________
>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>> 
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
> 
> _________________________________________________________________
> http://fastmail.ca/ - Fast Secure Web Email for Canadians
> 
> 

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From ame at esbs.u-strasbg.fr  Thu Dec  4 08:12:32 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Thu, 4 Dec 2003 14:12:32 +0100
Subject: [EMBOSS] remap and GCG mapplot
In-Reply-To: <3FCED187.00006F.07204@ns.interchange.ca>
References: <3FCED187.00006F.07204@ns.interchange.ca>
Message-ID: <84DB65C7-265B-11D8-B80D-0005024329A7@esbs.u-strasbg.fr>

Thanks for the information. I wrote to him to ask him TACG version 4 
which I think will very likely also solve my problems.
Jean-Christophe


Le 4 d?c. 03, ? 07:17, Stefanie Lager a ?crit :

> I don't know anything about MacOSX, but when I had problems with TACG
> on Linux Harry Mangalam sent me the latest TACG version 4.0, which
> solved my compilation problems.
>
> Stefanie
>
>> It looks good, but I tried to compiled it with MacOSX 10.3 and I
>> got a lot of errors...
>>
>> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
>>
>>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>>> for some of the GCG applications missing in EMBOSS. Like
>>>
>>> mapplot (tacg -l -s )
>>> map (tacg -T3,1 -sL )
>>> mapsort (tacg -cF2 )
>>> mapgel (tacg -g10 -s )
>>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>>>
>>> Stefanie
>>>
>>>> Hello,
>>>>
>>>> I am writing for a request for emboss. It would be great that
>>>> emboss could integrate something similar to the very useful (my
>>>> point of view) GCG's program MAPPLOT (a graphical representation
>>>> of a restriction map). I am sure that could be easily added to
>>>> emboss's remap or restrict.
>>>> With this feature added I would definitively not use anymore
>>>> GCG. Any idea. Thanks for the great job.
>>>> Jean-Christophe
>>>>
>>>> ________________________
>>>> Jean-Christophe Am?, PhD
>>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>>>> Structurale
>>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>>> P?le API
>>>> Parc d'innovation, Boulevard S?bastien Brant
>>>> BP 10413
>>>> 67412 ILLKIRCH CEDEX
>>>> France
>>>>
>>>> tel.: 33 3 90 24 47 05
>>>> Fax.: 33 3 90 24 46 86
>>>
>>> _________________________________________________________________
>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>>
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
>
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From louis at gtptech.com  Thu Dec  4 10:28:54 2003
From: louis at gtptech.com (Carole Louis)
Date: 04 Dec 2003 16:28:54 +0100
Subject: [EMBOSS] problem in my program
Message-ID: <1070551736.1392.49.camel@thym>

Hi,

I'm programming in EMBOSS 2.7.1 (not yet in EMBOSS 2.8.0) and I don't
understand why my program does not work. I'm looking for the error since
yesterday but I don't find it. The part of my program where is the
problem is :

      // obtention fin extremite terminale oligo gche
      // mise sequence1 dans tableau
      iterSeq1 = ajStrIter(res2->sequenceGche);
      while (!ajStrIterDone(iterSeq1))
       	{
	          c = ajStrIterGetK(iterSeq1);
	          tabSeq1[i] = c;
	 	        i++;
	 	        ajStrIterNext(iterSeq1);
	        }
      
      // Nucleotide extremite 3' de l'oligo gauche
      Nuc3OligGche = tabSeq1[lenSeq1-1];
      
  
      // obtention fin extremite terminale oligo dte 
      // sequence2 dans tableau
      iterSeq2 = ajStrIter(res2->sequenceDte);
      while (!ajStrIterDone(iterSeq2))
            	{
	              d = ajStrIterGetK(iterSeq2);
	              tabSeq2[j] = d;
	              j++;
	             ajStrIterNext(iterSeq2);
	             }
      
      
      // Nucleotide extremite 3' de l'oligo droite
      Nuc3OligDte = tabSeq2[lenSeq2-1];
   
      ajStrAssCI(&charT, "T",1);
      ajStrAssCI(&charA, "A",1);
           
      if ((ajStrMatchCaseC (charA,&Nuc3OligGche))||(ajStrMatchCaseC
(charT,&Nuc3OligGche)))
      	{
	        ajFmtPrintF(outf, "oligo gche finit par A ou T \n");
	        res2->score = res2->score - 1; 
      	}
      
      if ((ajStrMatchCaseC (charAbis,&Nuc3OligDte))||(ajStrMatchCaseC
(charTbis,&Nuc3OligDte)))
      	{
	        ajFmtPrintF(outf, "oligo dte finit par A ou T \n");
	        res2->score = res2->score - 1; 
      	}
 
There isn't any problem with the first buckle 1 (see in red) but my
program does'nt go is the buckle 2 (see in green) as it should do it and
as it do with the buckle 1.  Is someone can help me, please. I have no
more idea now and don't know what to do. May be my problem will appear
very clear for someone. I hope it, in fact.      :-) 
Thanks,
Carole Louis

        
  
	  



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From gtps5 at gtptech.com  Thu Dec  4 10:45:45 2003
From: gtps5 at gtptech.com (Carole Louis)
Date: 04 Dec 2003 16:45:45 +0100
Subject: [EMBOSS] problem in my program
In-Reply-To: <1070551736.1392.49.camel@thym>
References: <1070551736.1392.49.camel@thym>
Message-ID: <1070552752.1435.53.camel@thym>

I read my mail and I saw I made a mistake copying my program but I
change it and it 'is the good version below.

Le jeu 04/12/2003 ? 16:28, Carole Louis a ?crit :

    Hi, 
    
    I'm programming in EMBOSS 2.7.1 (not yet in EMBOSS 2.8.0) and I
    don't understand why my program does not work. I'm looking for the
    error since yesterday but I don't find it. The part of my program
    where is the problem is : 
    
          // obtention fin extremite terminale oligo gche
          // mise sequence1 dans tableau
          iterSeq1 = ajStrIter(res2->sequenceGche);
          while (!ajStrIterDone(iterSeq1))
           {
              c = ajStrIterGetK(iterSeq1);
              tabSeq1[i] = c;
            i++;
            ajStrIterNext(iterSeq1);
            }
          
          // Nucleotide extremite 3' de l'oligo gauche
          Nuc3OligGche = tabSeq1[lenSeq1-1];
          
      
          // obtention fin extremite terminale oligo dte 
          // sequence2 dans tableau
          iterSeq2 = ajStrIter(res2->sequenceDte);
          while (!ajStrIterDone(iterSeq2))
                {
                  d = ajStrIterGetK(iterSeq2);
                  tabSeq2[j] = d;
                  j++;
                 ajStrIterNext(iterSeq2);
                 }
          
          
          // Nucleotide extremite 3' de l'oligo droite
          Nuc3OligDte = tabSeq2[lenSeq2-1];
       
          ajStrAssCI(&charT, "T",1);
          ajStrAssCI(&charA, "A",1);
               
          if ((ajStrMatchCaseC (charA,&Nuc3OligGche))||(ajStrMatchCaseC
    (charT,&Nuc3OligGche)))
          {
            ajFmtPrintF(outf, "oligo gche finit par A ou T \n");
            res2->score = res2->score - 1; 
          }
          
          if ((ajStrMatchCaseC (charA,&Nuc3OligDte))||(ajStrMatchCaseC
    (charT,&Nuc3OligDte)))
          {
            ajFmtPrintF(outf, "oligo dte finit par A ou T \n");
            res2->score = res2->score - 1; 
          }
    
    There isn't any problem with the first buckle 1 (see in red) but my
    program does'nt go is the buckle 2 (see in green) as it should do it
    and as it do with the buckle 1.  Is someone can help me, please. I
    have no more idea now and don't know what to do. May be my problem
    will appear very clear for someone. I hope it, in fact.      :-) 
    Thanks, 
    Carole Louis 
    
            
      
      
    
    
    
    
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From gbottu at ben.vub.ac.be  Thu Dec  4 13:58:28 2003
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 4 Dec 2003 19:58:28 +0100
Subject: [EMBOSS] gap penalties for water
In-Reply-To: <3FCDF797.8020309@md.huji.ac.il>
References: <3FCDF797.8020309@md.huji.ac.il>
Message-ID: <20031204185828.GA11119@bigben.ulb.ac.be>


Well, there are two ways to compute a penalty for a gap of n positions :

<gap opening penalty> + (n - 1) * <gap extension penalty>
<gap penalty> + n * <gap length penalty>

The first way is used by EMBOSS and BLAST
The second way is used by GCG, Staden and CLUSTAL
fastA used for a long time the first way, but Prof. pearson decided 
recently to shift to the second

The two methods are basically equivalent (it depends on which values you 
choose) and you can discuss at infinitam and ad nauseam which is best.

	Regards,
	Guy Bottu
	Belgian EMBnet Node


From news at venturereporter.net  Wed Dec 10 14:01:38 2003
From: news at venturereporter.net (Venture Reporter)
Date: 10 Dec 2003 19:01:38 -0000
Subject: [EMBOSS] Venture Reporter Research: Two Biotech reports for only $395!
Message-ID: <20031210190138.26888.qmail@sfq4.venturereporter.net>

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From American_Biotechnology_Laboratory at xmr3.com  Thu Dec 11 11:52:00 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Thu, 11 Dec 2003 11:52:00 -0500
Subject: [EMBOSS] Laboratory Scientific Product Expo
Message-ID: <I-0-757640-19599867-2-9499-US2-E2B7AA44@xmr3.com>

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From American_Laboratory at xmr3.com  Thu Dec 11 11:57:15 2003
From: American_Laboratory at xmr3.com (American Laboratory)
Date: Thu, 11 Dec 2003 11:57:15 -0500
Subject: [EMBOSS] Laboratory Scientific Product Expo
Message-ID: <I-2-757641-19599724-2-27942-US2-E6FB86D2@xmr3.com>

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From OBJ at obj.org  Thu Dec 11 19:09:40 2003
From: OBJ at obj.org (OBJ)
Date: Fri, 12 Dec 2003 00:09:40 +0000
Subject: [EMBOSS] No minimo, =?ISO-8859-1?Q?d=EA?= o beneficio da
 =?ISO-8859-1?Q?d=FAvida!?=
Message-ID: <20031212000945.8760A7D6FE@mercury.hgmp.mrc.ac.uk>


Boas, antes de mais gostaria de informar que o seu email foi retirado de uma ou mais p?ginas
da Internet e que este seu email ser? apagado, logo ap?s o envio desta mensagem.

O que me faz enviar esta mensagem, ? muio simples, tenho estado a desenvolver um neg?cio independente
a partir de casa no ?ltmos 9 meses, o qual j? conhecia ? mais de 10 anos, mas s? h? 9 meses tive a
curiosidade e motivo para o analizar. Como podem entender abraceio-o e, gostaria de lhe dar a conhecer
esta oportunidade. Se por qualquer motivo os seus sonhos de estilo de vida lhe parecem cada vez
mais longinquos, se por algum motivo acha que, independentemente da sua idade, nunca os vai conseguir
alcan?ar, gostaria de lhe poder dar a analizar esta oportunidade.

Quantos de n?s trabalha-mos um vida inteira para construir algo e chega-mos ao fim da vida sem ter nada
ou tendo apenas uma parte muito pequena daquilo que ambiciona-mos.

Gostaria de lhe perguntar se estaria disposto(a), a apenas com algumas horas por semana, e fazendo um sacrificio e
esfor?o extra, durante os pr?ximo 3 a 4 anos, dedicar essas horas por semana e da? fazer crescer um
rendimento tal que n?o se teria de preocupar com a sua vida fincanceira.

O que me diz a poder ganhar 500? extra, juntando ao dinheiro que j? ganha, e fazer com que estes 500?
crescam de m?s pra m?s a uma velocidade impressionante. Estaria disposto a fazer esse esfor?o?

Se esta no minimo curioso para analizar esta oportunidade, ent?o contacte-me de forma a poder assitir
via internet a uma apresenta??o no conforto da sua casa, e talvez, quem sabe, come?ar a mudar algo na sua vida.

Fernanda Manuela
as1531033 at sapo.pt


From jack.leunissen at wur.nl  Fri Dec 12 07:07:37 2003
From: jack.leunissen at wur.nl (Jack Leunissen)
Date: Fri, 12 Dec 2003 13:07:37 +0100
Subject: [EMBOSS] restrict -alphabetic
Message-ID: <000601c3c0a8$8bd8b620$d930e089@bioinf01>

Dear EMBOSS gurus,
 
I don't understand the output of the RESTRICT program when using the
-ALPHABETIC option. The output is more or less alphabetically sorted,
but not completely. So the question remains: sorted alphabetically on
what?
 
Cheers,
Jack
 
 
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From American_Biotechnology_Laboratory at xmr3.com  Mon Dec 15 14:01:49 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Mon, 15 Dec 2003 14:01:49 -0500
Subject: [EMBOSS] ALA LabFusion 2004 Call for Papers
Message-ID: <I-8-757640-19670149-2-9499-US2-6577A7C6@xmr3.com>

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From brett.kaufman at mcgill.ca  Mon Dec 15 15:48:53 2003
From: brett.kaufman at mcgill.ca (Brett Kaufman)
Date: Mon, 15 Dec 2003 15:48:53 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
Message-ID: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca>

I have receive such fantastic and patient help from Tim Carver that I 
though I would submit experience back to the emboss boards.

standalone Jemboss EMBOSS-2.8.0 successfully installed:

All of this was done on 10.3.1 with the latest fink installed and 
working.  At the time, EMBOSS-2.8.0 wasn't available through fink, so 
it was downloaded and installed from command line.  To repeat my steps, 
you will need to be certain that libiconv, gd2, and libpng are current. 
Remember to run fink selfupdate and update all a time or two to be 
certain everything is completely there ;).

download emboss-2.8.0, and embassy components. Emboss will install in 
/usr/local, so I moved the downloaded folders to a new directory 
/usr/local/installers.  The original folder is needed after the 
install, so this make a permanent home for the EMBOSS-2.8.0 folder.  
gunzip and tar-xvf everything.

 >cd /usr/local/installers/EMBOSS-2.8.0/jemboss/utils
 >./install-jemboss-server.sh

The Java file for Panther is:
/System/Library/Frameworks/JavaVM.framework/Home

Accepting the default responses usually works, except for the png 
driver.  In this installation, use --with-pngdriver=/sw.

when prompted, move the decompressed embassy files to the new embassy 
folder in EMBOSS-2.8.0 within the installer.

when installation is finished, there a few things that are worth 
changing.

As panther uses bash, I used pico ~/.bashrc to make sure that I can run 
emboss  from any directory):
PATH=$PATH:/usr/local/emboss/bin

The runJemboss file needs to be modified; however, the prescribed 
modification on the web are for runJemboss.csh, which is from 
emboss-2.7.1, rather than runJemboss.sh, which you will be using.

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

remove the # on DYLD_LIBRARY_PATH...

Keep an eye open for word wrap issues.  Should you have launch issues, 
try pico -w and look for disconnect text.

I added Jemboss to the X11 menu:
Applications -> Customize
Name= Jemboss
Command= /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh
Shortcut=j
done

hitting command-j will launch the application if x11 is active.

Make sure to dl clustalw and install it in /usr/local/bin to get emma 
to work properly.

primer3: this is sort of ugly, but it works.
download primer3_0_9_test from the whitehead institute. gunzip and tar 
-xvf, then move to installers.
 >cd /usr/local/installers/primer3_0_9_test/src

I had to edit the Makefile using a hint from Alex Brown.
I removed the line:
LIBOPTS ='-static'
and then removed all references to $(LIBOPTS)

It has been suggested that you change CC=gcc to CC=CC, but I haven't.
 >make primer3
when finished, you can test
 >cd ../test
 >./primer_test.pl
Don't be totally dismayed if you see a FAILED during test after primer 
comparison.
if you ran the test, then
 >cd ../src
you need the primer3_core in the path of emboss, so copy it to 
emboss/bin
 >cp primer3_core /usr/local/emboss/bin
Seems to work for me from command line or Jemboss.  Let me know if this 
hack didn't cut it for you!

at this point it might be useful to build you locate database:
 >sudo /usr/libexec/locate.updatedb

Activating all the goodies:
you need to run:
aaextractindex, cutgextract, printsextract, prosextract, rebase
(there may be others that I ran, or other that I have yet to discover 
that I need to run).  I did this from commandline, but it looks like 
Jemboss will run them also.  Some of the target databases are in 
/usr/local/installers/EMBOSS-2.8.0/test/data, others have to be 
downloaded.  The appropriate source is on the corresponding help pages.




Current problems:
I have an display issue with .png files.  Plots and graphs made 
correctly, but they do not display properly in the results window.  If 
I save those displayed results, and open them in preview, they are 
fine; thus, it is a display issue only.

I hope this adequately thorough to provide some clues to any problems 
you are having with your install.

-Brett


????????????????????????????????????????????????????????
Brett Kaufman, Ph.D
3801 University
Rm 676
Montreal, QC H3A 2B4
Canada

brett.kaufman at mcgill.ca
(514) 398 8523
(514) 398 1509 (fax)
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From hsut5 at yahoo.com  Mon Dec 15 20:08:25 2003
From: hsut5 at yahoo.com (Tai Hsu)
Date: Mon, 15 Dec 2003 17:08:25 -0800 (PST)
Subject: [EMBOSS] suggestion of a new application
Message-ID: <20031216010825.55889.qmail@web20810.mail.yahoo.com>

Dear Sirs:

I like to offer a string alignment utility that have the advantages of
both of the "local alignement" and the "global alignment", and none of
their disadvantages. It's called Walking Tree method. Please let me
know how I can submit my offer.

Thanks,
Tai Hsu, Ph.D.

__________________________________
Do you Yahoo!?
New Yahoo! Photos - easier uploading and sharing.
http://photos.yahoo.com/


From brettkaufman at videotron.ca  Mon Dec 15 20:37:50 2003
From: brettkaufman at videotron.ca (Brett Kaufman)
Date: Mon, 15 Dec 2003 20:37:50 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
In-Reply-To: <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net>
References: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca> <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net>
Message-ID: <757B5350-2F68-11D8-AD83-000A95DA5C82@videotron.ca>

Koen,
Have you compiled Jemboss from the finkinstall?  Have you considered 
making a jemboss package for fink?

-Brett

On 15-Dec-03, at 7:59 PM, Koen van der Drift wrote:

> On Dec 15, 2003, at 3:48 PM, Brett Kaufman wrote:
>
>> All of this was done on 10.3.1 with the latest fink installed and 
>> working.  At the time, EMBOSS-2.8.0 wasn't available through fink,
>
> As the maintainer of EMBOSS I can inform you that 2.8.0 is now 
> available through fink (unstable tree).
>
> - Koen.
>



From kvddrift at earthlink.net  Mon Dec 15 20:39:30 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Mon, 15 Dec 2003 20:39:30 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
In-Reply-To: <6DFCEB9C-2F66-11D8-AD83-000A95DA5C82@mcgill.ca>
References: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca> <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net> <6DFCEB9C-2F66-11D8-AD83-000A95DA5C82@mcgill.ca>
Message-ID: <B10A997E-2F68-11D8-9B0B-003065A5FDCC@earthlink.net>


On Dec 15, 2003, at 8:23 PM, Brett Kaufman wrote:

> Have you compiled Jemboss from the finkinstall?  Have you considered 
> making a jemboss package for fink?
>

So far, 'no' to both questions. I use emboss-kaptain (also from fink) 
as a GUI.

- Koen.



From American_Biotechnology_Laboratory at xmr3.com  Tue Dec 16 09:31:25 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Tue, 16 Dec 2003 09:31:25 -0500
Subject: [EMBOSS] American Biotechnology Laboratory February 2004 
Message-ID: <I-4-757640-19816265-2-9499-US2-D30F19D2@xmr3.com>

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From Caroline.Barretto at rdls.nestle.com  Tue Dec 16 11:11:37 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Tue, 16 Dec 2003 17:11:37 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED50579E@chlsne01.nestle.com>

Dear all,
 
Did anybody notice that the seqret program seems to be limited by the number
of sequences to convert ? I am trying to convert 1 file containing 23000
genbank sequences into GCG format.
Do you have a suggestion for that ?
 
Thank you very much,
 
Regards,
 
Caroline.
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From simon.andrews at bbsrc.ac.uk  Tue Dec 16 11:46:39 2003
From: simon.andrews at bbsrc.ac.uk (simon andrews (BI))
Date: Tue, 16 Dec 2003 16:46:39 -0000
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C3E@bi-exsrv1.iapc.bbsrc.ac.uk>


-----Original Message-----
From: Barretto,Caroline,LAUSANNE,NRC/BAS [mailto:Caroline.Barretto at rdls.nestle.com] 
Sent: 16 December 2003 16:12
To: emboss at embnet.org
Subject: [EMBOSS] Does seqret have limitations ?


> Dear all,
> 
> Did anybody notice that the seqret program seems to 
> be limited by the number of sequences to convert ? I 
> am trying to convert 1 file containing 23000 genbank 
> sequences into GCG format.
>
> Do you have a suggestion for that ?

Seqret is not limited by number of files.  I routinely pass the whole of EMBL through seqret and it works fine.  What error do you get when seqret stops?  Could it just be that there is a malformed entry part way through your file?

Is the file you are trying to convert >2Gb in size?  If so this could be the reason for the failure rather than seqret being limited by the number of sequences.  In this case though I thought that the failure would happen when the file was first opened and not after a certain number of sequences had passed through.

If the problem is a large file you might be able to get round this by using a pipe to get information into seqret.  Try

cat your_genbank_file.gb | seqret -filter -osf gcg > your_gcg_file.gcg

This should work as long as your OS version of cat and your shell can handle large files.

Hope this helps

Simon.


From Caroline.Barretto at rdls.nestle.com  Tue Dec 16 12:26:53 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Tue, 16 Dec 2003 18:26:53 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED50579F@chlsne01.nestle.com>

Dear Simon,

I don't receive any error from seqret, it simply stops just as if it was
correctly finished. 
The file is not bigger than 2Gb:
$ du -sk file.gbk
74680   file.gbk

Even with the cat command you sent me, I only get 17143 sequences formatted
in GCG format. (it is the same if I try to convert in fasta format)

$ grep -c "Check" file.gcg
17143
$ grep -c "LOCUS" file.gbk
26045

$ seqret file.gbk -osformat fasta -outseq test
Reads and writes (returns) sequences
$ grep -c ">" test
17143

If anybody has an idea...

Thanks a lot,

Caroline.



-----Original Message-----
From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
Sent: mardi, 16. d?cembre 2003 17:47
To: 'emboss at embnet.org'
Subject: RE: [EMBOSS] Does seqret have limitations ?



-----Original Message-----
From: Barretto,Caroline,LAUSANNE,NRC/BAS
[mailto:Caroline.Barretto at rdls.nestle.com] 
Sent: 16 December 2003 16:12
To: emboss at embnet.org
Subject: [EMBOSS] Does seqret have limitations ?


> Dear all,
> 
> Did anybody notice that the seqret program seems to 
> be limited by the number of sequences to convert ? I 
> am trying to convert 1 file containing 23000 genbank 
> sequences into GCG format.
>
> Do you have a suggestion for that ?

Seqret is not limited by number of files.  I routinely pass the whole of
EMBL through seqret and it works fine.  What error do you get when seqret
stops?  Could it just be that there is a malformed entry part way through
your file?

Is the file you are trying to convert >2Gb in size?  If so this could be the
reason for the failure rather than seqret being limited by the number of
sequences.  In this case though I thought that the failure would happen when
the file was first opened and not after a certain number of sequences had
passed through.

If the problem is a large file you might be able to get round this by using
a pipe to get information into seqret.  Try

cat your_genbank_file.gb | seqret -filter -osf gcg > your_gcg_file.gcg

This should work as long as your OS version of cat and your shell can handle
large files.

Hope this helps

Simon.
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From luqiang at scbit.org  Tue Dec 16 21:20:32 2003
From: luqiang at scbit.org (Lu Qiang)
Date: Wed, 17 Dec 2003 10:20:32 +0800
Subject: [EMBOSS] Pepinfo's postscript output
Message-ID: <20031217021745.B5A2E7D790@mercury.hgmp.mrc.ac.uk>

Guys,

When I use pepinfo as following:
pepinfo -inseq PCNA.fasta -graph ps -outfile pepinfo.out
pepinfo.ps is created. However, the two-page graph output could not be showed in GSView. Error is listed as:
DSC Error
EPS files may have 0 or 1 pages. This 'EPS' file has
more than this and so is not an EPS file.
You cannot use 'Print To' ??Encapsulated PostScriptFile' for
print multipage files. The correct method is to connect 
the printer to FILE: or to select 'Print to File'.
..

Could anyone tell me how to process this error, and thus see the 2nd page in the pepinfo.ps?

regards,

Lu Qiang
luqiang at scbit.org
2003-12-17




From stefanielager at fastmail.ca  Wed Dec 17 01:05:56 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 17 Dec 2003 01:05:56 -0500 (EST)
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <3FDFF244.000199.02566@ns.interchange.ca>

It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
> 
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
> 
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
> 
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
> 
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
> 
> If anybody has an idea...
> 
> Thanks a lot,
> 
> Caroline.
> 
> 
> 
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
> 
> 
> 
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
> 
> 
>> Dear all,
>> 
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>> 
>> Do you have a suggestion for that ?
> 
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
> 
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
> 
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
> 
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
> 
> This should work as long as your OS version of cat and your shell
> can handle large files.
> 
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From David.Bauer at SCHERING.DE  Wed Dec 17 02:44:23 2003
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 17 Dec 2003 08:44:23 +0100
Subject: Antwort: [EMBOSS] Pepinfo's postscript output
Message-ID: <OF56828184.DB77A61A-ONC1256DFF.00297B08@schering.de>


Hi Lu,

which version of GSview are you using? I just tested it with 4.4 (output
from EMBOSS2.8.0).
GSview also complains (correctly) about the second page but it can also
show this page with the hydropathy plots.
Workarounds:
1) tell pepinfo to produce only one graph
2) open pepinfo.ps with a text editor and remove the line with the bounding
box definition.

Hope this helps,
David.


                                                                                                               
                      "Lu Qiang"                                                                               
                      <luqiang at scbit.o                                                                         
                      rg>                      An:      "emboss at embnet.org" <emboss at embnet.org>                
                      Gesendet von:            Kopie:                                                          
                      owner-emboss at hgm         Thema:   [EMBOSS] Pepinfo's postscript output                   
                      p.mrc.ac.uk                                                                              
                                                                                                               
                                                                                                               
                      17.12.03 03:20                                                                           
                                                                                                               
                                                                                                               




Guys,

When I use pepinfo as following:
pepinfo -inseq PCNA.fasta -graph ps -outfile pepinfo.out
pepinfo.ps is created. However, the two-page graph output could not be
showed in GSView. Error is listed as:
DSC Error
EPS files may have 0 or 1 pages. This 'EPS' file has
more than this and so is not an EPS file.
You cannot use 'Print To' ??Encapsulated PostScriptFile' for
print multipage files. The correct method is to connect
the printer to FILE: or to select 'Print to File'.
..

Could anyone tell me how to process this error, and thus see the 2nd page
in the pepinfo.ps?

regards,

Lu Qiang
luqiang at scbit.org
2003-12-17






From David.Bauer at SCHERING.DE  Wed Dec 17 02:58:36 2003
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 17 Dec 2003 08:58:36 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <OFD262E18F.1898DE09-ONC1256DFF.002AAF88@schering.de>


Another explanation could be if there is a Contig type entry in the GenBank
File.
The Contig GenBank entries do not contain any sequence. The feature table
contains only references to other sequence entries.
Seqret can not handle this type of virtual sequence entries.

David.


                                                                                                               
                      "Stefanie Lager"                                                                         
                      <stefanielager at f                                                                         
                      astmail.ca>              An:      emboss at embnet.org                                      
                      Gesendet von:            Kopie:                                                          
                      owner-emboss at hgm         Thema:   RE: [EMBOSS] Does seqret have limitations ?            
                      p.mrc.ac.uk                                                                              
                                                                                                               
                                                                                                               
                      17.12.03 07:05                                                                           
                                                                                                               
                                                                                                               




It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
>
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
>
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
>
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
>
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
>
> If anybody has an idea...
>
> Thanks a lot,
>
> Caroline.
>
>
>
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
>
>
>
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
>
>
>> Dear all,
>>
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>>
>> Do you have a suggestion for that ?
>
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
>
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
>
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
>
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
>
> This should work as long as your OS version of cat and your shell
> can handle large files.
>
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians






From Caroline.Barretto at rdls.nestle.com  Wed Dec 17 05:27:39 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Wed, 17 Dec 2003 11:27:39 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED021E351F@chlsne01.nestle.com>

Thank you very much to everybody, the problem was, as some of you suspected,
in the genbank file...

Best wishes

Caroline.

 

                      "Stefanie Lager"

                      <stefanielager at f

                      astmail.ca>              An:      emboss at embnet.org

                      Gesendet von:            Kopie:

                      owner-emboss at hgm         Thema:   RE: [EMBOSS] Does
seqret have limitations ?            
                      p.mrc.ac.uk

 

 

                      17.12.03 07:05

 

 





It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
>
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
>
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
>
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
>
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
>
> If anybody has an idea...
>
> Thanks a lot,
>
> Caroline.
>
>
>
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
>
>
>
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
>
>
>> Dear all,
>>
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>>
>> Do you have a suggestion for that ?
>
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
>
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
>
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
>
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
>
> This should work as long as your OS version of cat and your shell
> can handle large files.
>
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



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From georg.otto at tuebingen.mpg.de  Thu Dec 18 11:18:25 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Thu, 18 Dec 2003 17:18:25 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
Message-ID: <web-7083690@tuebingen.mpg.de>

Hi,

I tried to compile EMBOSS on a new computer running Mac OSX
10.3 unfortunately, the compile process aborts with the
error message:

/bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
 aaindexextract.o ../nucleus/libnucleus.la
../ajax/libajaxg.la ../ajax/libajax.la
../plplot/libplplot.la -lX11  -lm 
gcc -O2 -o .libs/aaindexextract aaindexextract.o
 ../nucleus/.libs/libnucleus.dylib
../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1


As I understand, EMBOSS has problems with Mac?s X11. Is
there any way to get around this.

Any help will be highly appreciated.

Cheers,

Georg

-- 
Georg Wilhelm Otto
Max-Planck-Institute for Developmental Biology
Department 3 - Genetics
Spemannstrasse 35
D-72076 Tuebingen (Germany)
phone:   +49-7071-601393
e-mail: georg.otto at tuebingen.mpg.de


From ame at esbs.u-strasbg.fr  Thu Dec 18 11:51:32 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Thu, 18 Dec 2003 17:51:32 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <web-7083690@tuebingen.mpg.de>
References: <web-7083690@tuebingen.mpg.de>
Message-ID: <6EE19D7E-317A-11D8-8CA7-0005024329A7@esbs.u-strasbg.fr>

Hi Georg,

I have the same configuration and didn't have any problem compiling it. 
You should get from the developer tools CD the X11SDK which is an 
option to install.

My computer is even not supported by panther (a powerbook wallstreet + 
G4 upgrade) and I have no problem with it at all.
Sincerely,
Jean-Christophe


Le 18 d?c. 03, ? 17:18, Georg Otto a ?crit :

> Hi,
>
> I tried to compile EMBOSS on a new computer running Mac OSX
> 10.3 unfortunately, the compile process aborts with the
> error message:
>
> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>  aaindexextract.o ../nucleus/libnucleus.la
> ../ajax/libajaxg.la ../ajax/libajax.la
> ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>  ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
>
> As I understand, EMBOSS has problems with Mac?s X11. Is
> there any way to get around this.
>
> Any help will be highly appreciated.
>
> Cheers,
>
> Georg
>
> -- 
> Georg Wilhelm Otto
> Max-Planck-Institute for Developmental Biology
> Department 3 - Genetics
> Spemannstrasse 35
> D-72076 Tuebingen (Germany)
> phone:   +49-7071-601393
> e-mail: georg.otto at tuebingen.mpg.de
>
>
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From brettkaufman at videotron.ca  Thu Dec 18 20:35:13 2003
From: brettkaufman at videotron.ca (Brett Kaufman)
Date: Thu, 18 Dec 2003 20:35:13 -0500
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <web-7083690@tuebingen.mpg.de>
References: <web-7083690@tuebingen.mpg.de>
Message-ID: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>

Georg,
How were you installing emboss, from fink or by what method?

Were there errors earlier in the install?

I have emboss running on 10.3, so far, so good.  Have you might need 
full dev tools and x11 sdk.

-Brett
On 18-Dec-03, at 11:18 AM, Georg Otto wrote:

> Hi,
>
> I tried to compile EMBOSS on a new computer running Mac OSX
> 10.3 unfortunately, the compile process aborts with the
> error message:
>
> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>  aaindexextract.o ../nucleus/libnucleus.la
> ../ajax/libajaxg.la ../ajax/libajax.la
> ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>  ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
>
> As I understand, EMBOSS has problems with Mac?s X11. Is
> there any way to get around this.
>
> Any help will be highly appreciated.
>
> Cheers,
>
> Georg
>
> -- 
> Georg Wilhelm Otto
> Max-Planck-Institute for Developmental Biology
> Department 3 - Genetics
> Spemannstrasse 35
> D-72076 Tuebingen (Germany)
> phone:   +49-7071-601393
> e-mail: georg.otto at tuebingen.mpg.de
>



From georg.otto at tuebingen.mpg.de  Fri Dec 19 05:47:02 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Fri, 19 Dec 2003 11:47:02 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>
Message-ID: <ADB7FB24-3210-11D8-BF4B-003065C99468@tuebingen.mpg.de>

Dear all,

I think that I could solve the problem of compiling and running EMBOSS 
on Mac OS 10.3, thanks to the help of Jean-Christophe Ame and Alan 
Bleasby. On my Computer, X11 was installed but not X11 SDK. This comes 
as an extra package on the developer CD. I installed it, then i 
configured and compiled EMBOSS (I used the distribution from the EMBOSS 
website, not the fink). It compiled without problems and it runs now.

Cheers,

Georg


On Friday, December 19, 2003, at 02:35 AM, Brett Kaufman wrote:

> Georg,
> How were you installing emboss, from fink or by what method?
>
> Were there errors earlier in the install?
>
> I have emboss running on 10.3, so far, so good.  Have you might need 
> full dev tools and x11 sdk.
>
> -Brett
> On 18-Dec-03, at 11:18 AM, Georg Otto wrote:
>
>> Hi,
>>
>> I tried to compile EMBOSS on a new computer running Mac OSX
>> 10.3 unfortunately, the compile process aborts with the
>> error message:
>>
>> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>>  aaindexextract.o ../nucleus/libnucleus.la
>> ../ajax/libajaxg.la ../ajax/libajax.la
>> ../plplot/libplplot.la -lX11  -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>>  ../nucleus/.libs/libnucleus.dylib
>> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
>> ../plplot/.libs/libplplot.dylib -lX11 -lm
>> ld: can't locate file for: -lX11
>> make[2]: *** [aaindexextract] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>> As I understand, EMBOSS has problems with Mac?s X11. Is
>> there any way to get around this.
>>
>> Any help will be highly appreciated.
>>
>> Cheers,
>>
>> Georg
>>
>> -- 
>> Georg Wilhelm Otto
>> Max-Planck-Institute for Developmental Biology
>> Department 3 - Genetics
>> Spemannstrasse 35
>> D-72076 Tuebingen (Germany)
>> phone:   +49-7071-601393
>> e-mail: georg.otto at tuebingen.mpg.de
>>
>



From georg.otto at tuebingen.mpg.de  Fri Dec 19 05:47:02 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Fri, 19 Dec 2003 11:47:02 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>
Message-ID: <ADB7FB24-3210-11D8-BF4B-003065C99468@tuebingen.mpg.de>

Dear all,

I think that I could solve the problem of compiling and running EMBOSS 
on Mac OS 10.3, thanks to the help of Jean-Christophe Ame and Alan 
Bleasby. On my Computer, X11 was installed but not X11 SDK. This comes 
as an extra package on the developer CD. I installed it, then i 
configured and compiled EMBOSS (I used the distribution from the EMBOSS 
website, not the fink). It compiled without problems and it runs now.

Cheers,

Georg


On Friday, December 19, 2003, at 02:35 AM, Brett Kaufman wrote:

> Georg,
> How were you installing emboss, from fink or by what method?
>
> Were there errors earlier in the install?
>
> I have emboss running on 10.3, so far, so good.  Have you might need 
> full dev tools and x11 sdk.
>
> -Brett
> On 18-Dec-03, at 11:18 AM, Georg Otto wrote:
>
>> Hi,
>>
>> I tried to compile EMBOSS on a new computer running Mac OSX
>> 10.3 unfortunately, the compile process aborts with the
>> error message:
>>
>> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>>  aaindexextract.o ../nucleus/libnucleus.la
>> ../ajax/libajaxg.la ../ajax/libajax.la
>> ../plplot/libplplot.la -lX11  -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>>  ../nucleus/.libs/libnucleus.dylib
>> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
>> ../plplot/.libs/libplplot.dylib -lX11 -lm
>> ld: can't locate file for: -lX11
>> make[2]: *** [aaindexextract] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>> As I understand, EMBOSS has problems with Mac?s X11. Is
>> there any way to get around this.
>>
>> Any help will be highly appreciated.
>>
>> Cheers,
>>
>> Georg
>>
>> -- 
>> Georg Wilhelm Otto
>> Max-Planck-Institute for Developmental Biology
>> Department 3 - Genetics
>> Spemannstrasse 35
>> D-72076 Tuebingen (Germany)
>> phone:   +49-7071-601393
>> e-mail: georg.otto at tuebingen.mpg.de
>>
>



From aengus.stewart at cancer.org.uk  Wed Dec 24 07:01:21 2003
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Wed, 24 Dec 2003 12:01:21 +0000
Subject: [EMBOSS] Jemboss updating
In-Reply-To: <20031204185828.GA11119@bigben.ulb.ac.be>
References: <3FCDF797.8020309@md.huji.ac.il> <20031204185828.GA11119@bigben.ulb.ac.be>
Message-ID: <3FE98011.5080701@cancer.org.uk>

Hi, 

Would it be possible to clarify for me what is required to update JEMBOSS?

I am just getting round to updating EMBOSS/Jemboss.

Are there any parts of the installation process that need to be rerun from my previous full install for client-server access with EMBOSS 2.7.1/ Jemboss 1.1?

Or would just building EMBOSS 2.8 and placing the JARS for Jemboss 1.2.1 in the correct place be enough?


Regards
Aengus


-- 
----------------------------------------------------------------------------
Aengus Stewart
Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
----------------------------------------------------------------------------



From tcarver at rfcgr.mrc.ac.uk  Sat Dec 27 07:56:31 2003
From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver)
Date: Sat, 27 Dec 2003 12:56:31 +0000 (GMT)
Subject: [EMBOSS] Jemboss updating
In-Reply-To: <3FE98011.5080701@cancer.org.uk>
Message-ID: <Pine.SOL.4.44.0312271254160.13200-100000@bromine>


Hi Aengus

The easiest way to do this is to start from scratch, i.e. stop the
tomcat server and remove the old copy and allow the installation script
to install emboss/jemboss etc.

Cheers
Tim

Tim Carver
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: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Wed, 24 Dec 2003, Aengus Stewart wrote:

> Hi,
>
> Would it be possible to clarify for me what is required to update JEMBOSS?
>
> I am just getting round to updating EMBOSS/Jemboss.
>
> Are there any parts of the installation process that need to be rerun
> from my previous full install for client-server access with EMBOSS
> 2.7.1/ Jemboss 1.1?
>
>  Or would just building EMBOSS 2.8 and placing the JARS for Jemboss
> 1.2.1 in the correct place be enough?
>
>
> Regards
> Aengus
>
>
> --
> ----------------------------------------------------------------------------
> Aengus Stewart
> Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
> Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
> ----------------------------------------------------------------------------
>



From ranrub at md.huji.ac.il  Sun Dec 28 11:03:44 2003
From: ranrub at md.huji.ac.il (Ran Rubinstein)
Date: Sun, 28 Dec 2003 18:03:44 +0200
Subject: [EMBOSS] Updating Emboss w/ SRS as gui
Message-ID: <000101c3cd5c$2b4d2ff0$7ea74084@sauron>

We are running EMBOSS 2.7.1 and SRS 7.1.1 (academic) as both the database
and a web front end. Does anyone have experience with newer emboss 2.8 and
SRS? Are the icarus (.i) files provided with SRS for using EMBOSS compatible
with the new version?

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



From kvddrift at earthlink.net  Mon Dec 29 12:30:41 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Mon, 29 Dec 2003 12:30:41 -0500
Subject: [EMBOSS] plplot question
Message-ID: <B98C5493-3A24-11D8-9AF6-003065A5FDCC@earthlink.net>

Hi,

Will it be a problem if I install emboss when an existing plplot 
package is already installed? If yes, is there a way to disable the 
plplot that comes with emboss from being installed so that emboss will 
use the already installed plplot?



thanks,

- Koen.




From henrikki.almusa at helsinki.fi  Mon Dec  1 11:54:49 2003
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Mon, 1 Dec 2003 13:54:49 +0200
Subject: [EMBOSS] EMBOSS 2.8.0 released
In-Reply-To: <200311301704.hAUH4tei000865@bromine.hgmp.mrc.ac.uk>
References: <200311301704.hAUH4tei000865@bromine.hgmp.mrc.ac.uk>
Message-ID: <200312011354.49516.henrikki.almusa@helsinki.fi>

On Sunday 30 November 2003 19:04, Alan Bleasby wrote:
> EMBOSS 2.8.0 is available for download from:
>
>   http://www.uk.embnet.org/Software/EMBOSS
>   ftp://ftp.uk.embnet.org/pub/EMBOSS
>
<snip>
>
> EMBASSY
>
> Note that, because of the ACD changes mentioned above, those sites who
> install the EMBASSY packages (also in ftp://ftp.uk.embnet.org/pub/EMBOSS/)
> will need to re-ftp and build them.

Is there any info on whether (and if so, when)  the newer version of phylip 
(3.6) is going to be embassified? In given directory there is only the older 
version (3.57c).

Thanks,
-- 
Henrikki Almusa


From chalaouxfr at wanadoo.fr  Tue Dec  2 11:55:26 2003
From: chalaouxfr at wanadoo.fr (fr chalaoux)
Date: Tue, 2 Dec 2003 12:55:26 +0100
Subject: [EMBOSS] cirdna problem on macosx
Message-ID: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>

Hi all,

As noted in  
http://www.mail-archive.com/fink-devel at lists.sourceforge.net/ 
msg06607.html , I confirm the problem.

It even subsists in EMBOSS 2.8.0 ...

Simon



From pmr at ebi.ac.uk  Tue Dec  2 12:06:37 2003
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 02 Dec 2003 12:06:37 +0000
Subject: [EMBOSS] cirdna problem on macosx
In-Reply-To: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>
References: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr>
Message-ID: <3FCC804D.30609@ebi.ac.uk>

fr chalaoux wrote:

> Hi all,
> 
> As noted in  
> http://www.mail-archive.com/fink-devel at lists.sourceforge.net/ 
> msg06607.html , I confirm the problem.
> 
> It even subsists in EMBOSS 2.8.0 ...

cirdna and lindna have some fixed array sizes which need fixing for some 
systems (and, as it happens, for valgrind memory tests).

Non-urgent (cirdna and lindna are not, as faras I am aware, highly 
used), so to be fixed in a future release... but quite soon.

As a quick fix, you can reduce MAXLABELS and perhaps MAXGROUPS in 
cirdna.c and lindna.c

Hope that helps,

Peter Rice




From kvddrift at earthlink.net  Tue Dec  2 22:19:30 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Tue, 2 Dec 2003 17:19:30 -0500
Subject: [EMBOSS] cirdna problem on macosx
In-Reply-To: <3FCC804D.30609@ebi.ac.uk>
References: <6B2E2E70-24BE-11D8-AAC4-000393AF484C@wanadoo.fr> <3FCC804D.30609@ebi.ac.uk>
Message-ID: <992CCEDC-2515-11D8-B643-003065A5FDCC@earthlink.net>


On Dec 2, 2003, at 7:06 AM, Peter Rice wrote:

> cirdna and lindna have some fixed array sizes which need fixing for 
> some systems (and, as it happens, for valgrind memory tests).
>
> Non-urgent (cirdna and lindna are not, as faras I am aware, highly 
> used), so to be fixed in a future release... but quite soon.
>
> As a quick fix, you can reduce MAXLABELS and perhaps MAXGROUPS in 
> cirdna.c and lindna.c
>


I am the maintainer of EMBOSS for fink. I have patched EMBOSS for fink 
that solves the above problem. Let me know if you want the updated info 
and patch file (for EMBOSS 2.8.0). I will submit them to fink, and 
hopefully they will be available in the tree asap.

- Koen.



From stefanielager at fastmail.ca  Wed Dec  3 07:17:18 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 3 Dec 2003 02:17:18 -0500 (EST)
Subject: [EMBOSS] siRNA improvements 
Message-ID: <3FCD8DFE.000201.00920@ns.interchange.ca>

Hi,

It would be nice if the EMBOSS application sirna could incorporate
simple calculation of free energy, to improve the siRNA design. Lately
several reports on siRNA design (reviewed in Silva et al 2003) have
showed the importance of making the 5' end of the antisense strand
less stable than the 3' end (Schwarz et al 2003). Also the center part
should show a lower internal stability (Khvorova et al 2003). Simple
energy profiles can be calculated by the method of Mathews et al
(Mathews et al 1999). Several of the commercial siRNA design servers
have already incorporated free energy parameters in the design, and it
would really be nice to have an alternative.

Stefanie


Silva JM, Sachidanandam R, Hannon GJ.
Free energy lights the path toward more effective RNAi  
Nat. Genet. 2003, 35:303-305.

Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD. 
Asymmetry in the assembly of the RNAi enzyme complex.
Cell. 2003 115:199-208.

Khvorova A, Reynolds A, Jayasena SD. 
Functional siRNAs and miRNAs exhibit strand bias.
Cell. 2003 115:209-216.

Mathews DH, Sabina J, Zuker M, Turner DH. 
Expanded sequence dependence of thermodynamic parameters improves
prediction of RNA secondary structure.
J Mol Biol. 1999 288:911-940.


_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From henrikki.almusa at helsinki.fi  Wed Dec  3 09:12:09 2003
From: henrikki.almusa at helsinki.fi (Henrikki Almusa)
Date: Wed, 3 Dec 2003 11:12:09 +0200
Subject: [EMBOSS] Jemboss dan+emma
Message-ID: <200312031112.09865.henrikki.almusa@helsinki.fi>

Hello,

I'm currently using emboss 2.8.0 and also jemboss as stand-alone client. I 
have problem with Dan and Emma. 

Dan. It can be run, but no output was produced. The window (view result) is 
empty and if I try to save trace is produced.

Emma. If run without pressing "load sequence attributes" it also will have 
empty result. Pressing the button will produce the trace.

Both of these work on commandline without problems. Both traces are in same 
file.

Thanks,
-- 
Henrikki Almusa
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From ame at esbs.u-strasbg.fr  Wed Dec  3 09:45:56 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Wed, 3 Dec 2003 10:45:56 +0100
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <7E4502ED-2575-11D8-AE7F-0005024329A7@esbs.u-strasbg.fr>

Hello,

I am writing for a request for emboss. It would be great that emboss 
could integrate something similar to the very useful (my point of view) 
GCG's program MAPPLOT (a graphical representation of a restriction 
map). I am sure that could be easily added to emboss's remap or 
restrict.
With this feature added I would definitively not use anymore GCG.
Any idea. Thanks for the great job.
Jean-Christophe

________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From gwilliam at hgmp.mrc.ac.uk  Wed Dec  3 09:49:06 2003
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Wed, 03 Dec 2003 09:49:06 +0000
Subject: [EMBOSS] siRNA improvements
References: <3FCD8DFE.000201.00920@ns.interchange.ca>
Message-ID: <3FCDB192.62A98DC8@hgmp.mrc.ac.uk>

Thanks for the suggestions.
I'll take a look.
Gary

Stefanie Lager wrote:
> 
> Hi,
> 
> It would be nice if the EMBOSS application sirna could incorporate
> simple calculation of free energy, to improve the siRNA design. Lately
> several reports on siRNA design (reviewed in Silva et al 2003) have
> showed the importance of making the 5' end of the antisense strand
> less stable than the 3' end (Schwarz et al 2003). Also the center part
> should show a lower internal stability (Khvorova et al 2003). Simple
> energy profiles can be calculated by the method of Mathews et al
> (Mathews et al 1999). Several of the commercial siRNA design servers
> have already incorporated free energy parameters in the design, and it
> would really be nice to have an alternative.
> 
> Stefanie
> 
> Silva JM, Sachidanandam R, Hannon GJ.
> Free energy lights the path toward more effective RNAi
> Nat. Genet. 2003, 35:303-305.
> 
> Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD.
> Asymmetry in the assembly of the RNAi enzyme complex.
> Cell. 2003 115:199-208.
> 
> Khvorova A, Reynolds A, Jayasena SD.
> Functional siRNAs and miRNAs exhibit strand bias.
> Cell. 2003 115:209-216.
> 
> Mathews DH, Sabina J, Zuker M, Turner DH.
> Expanded sequence dependence of thermodynamic parameters improves
> prediction of RNA secondary structure.
> J Mol Biol. 1999 288:911-940.
> 
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians

-- 
Gary Williams	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: name at rfcgr.mrc.ac.uk	Web: http://www.rfcgr.mrc.ac.uk


From shrish at ccmb.res.in  Wed Dec  3 09:04:45 2003
From: shrish at ccmb.res.in (Shrish Tiwari)
Date: Wed, 3 Dec 2003 14:34:45 +0530
Subject: [EMBOSS] MFOLD
Message-ID: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>

Hi!

Is it possible to include MFOLD, for computing DNA/RNA folds into EMBOSS?

Shrish


______________________________________________________________________
Dr. Shrish Tiwari
BIC, Centre for Cellular and Molecular Biology
Uppal Road, Hyderabad - 500 007
Phone: 91-40-7192776 (work), 91-40-7156603 (home)
email: shrish at ccmb.res.in
______________________________________________________________________



From stefanielager at fastmail.ca  Wed Dec  3 13:08:30 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 3 Dec 2003 08:08:30 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCDE04E.000011.77674@ns.interchange.ca>

The program TACG ( http://tacg.sourceforge.net/) can substitute for
some of the GCG applications missing in EMBOSS. Like 

mapplot (tacg -l -s )
map (tacg -T3,1 -sL )
mapsort (tacg -cF2 )
mapgel (tacg -g10 -s )
findpatterns (tacg -S2 -R 'path/to/a/pattern/file )

Stefanie

> Hello,
> 
> I am writing for a request for emboss. It would be great that
> emboss could integrate something similar to the very useful (my
> point of view) GCG's program MAPPLOT (a graphical representation
> of a restriction map). I am sure that could be easily added to
> emboss's remap or restrict.
> With this feature added I would definitively not use anymore GCG.
> Any idea. Thanks for the great job.
> Jean-Christophe
> 
> ________________________
> Jean-Christophe Am?, PhD
> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
> Structurale
> ?cole Sup?rieure de Biotechnologie de Strasbourg
> P?le API
> Parc d'innovation, Boulevard S?bastien Brant
> BP 10413
> 67412 ILLKIRCH CEDEX
> France
> 
> tel.: 33 3 90 24 47 05
> Fax.: 33 3 90 24 46 86

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From gilal at md.huji.ac.il  Wed Dec  3 14:47:51 2003
From: gilal at md.huji.ac.il (Gila Lithwick)
Date: Wed, 03 Dec 2003 16:47:51 +0200
Subject: [EMBOSS] water problems
Message-ID: <3FCDF797.8020309@md.huji.ac.il>

Hello,

I wasn't sure which mailing list this e-mail is more appropriate for, so 
I've sent it to both...

I have been using EMBOSS, and noticed the following problems with water:

1) Water does not give a gap extension penalty for the first gap.  This 
is not how gaps are generally penalized.
For example, the alignment between tttttcccaaaaa and tttttaaaaa is:
seq1               1 tttttcccaaaaa     13
                     |||||   |||||
seq2               1 ttttt---aaaaa     10
EMBOSS scores this 39, however the score should be 10*5-3*0.5-10=38.5
Is this correct?

2) Since the default gap extension penalty is so low (0.5), water often 
gives very long alignments.  A slightly higher gap penalty (for example 
1) gives better alignments - maybe it would be better to make this the 
default.

3) It would be very useful if there was a way to assess significance of 
pairwise alignments, such as the -rand option in gcg.  It is possible, 
of course, to do each step (shuffling one sequence, aligning, and 
calculating the mean and standard deviation) separately.  However, for 
users that don't know how to program, this isn't simple.

Thank you,
Gila.



From lmullan at hgmp.mrc.ac.uk  Wed Dec  3 14:56:10 2003
From: lmullan at hgmp.mrc.ac.uk (Lisa Mullan)
Date: Wed, 3 Dec 2003 14:56:10 +0000 (GMT)
Subject: [EMBOSS] Re: [EMBOSS-BUG] water problems
In-Reply-To: <3FCDF797.8020309@md.huji.ac.il>
Message-ID: <Pine.SOL.4.44.0312031453520.3443-100000@bromine>

Hi!

EMBOSS is scorring it correctly. You have three gaps in thie alignment.
The first gap incurs a penalty of ten for opeing the gap. And then the
subsequent gaps incur penalties of 0.5 each therefore the calculation is:

(10*5)-10-(2*0.5) = 39

I think you got over zealous with your extensions!!

Lisa

Lisa Mullan
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: lmullan at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk

On Wed, 3 Dec 2003, Gila Lithwick wrote:

> Hello,
>
> I wasn't sure which mailing list this e-mail is more appropriate for, so
> I've sent it to both...
>
> I have been using EMBOSS, and noticed the following problems with water:
>
> 1) Water does not give a gap extension penalty for the first gap.  This
> is not how gaps are generally penalized.
> For example, the alignment between tttttcccaaaaa and tttttaaaaa is:
> seq1               1 tttttcccaaaaa     13
>                      |||||   |||||
> seq2               1 ttttt---aaaaa     10
> EMBOSS scores this 39, however the score should be 10*5-3*0.5-10=38.5
> Is this correct?
>
> 2) Since the default gap extension penalty is so low (0.5), water often
> gives very long alignments.  A slightly higher gap penalty (for example
> 1) gives better alignments - maybe it would be better to make this the
> default.
>
> 3) It would be very useful if there was a way to assess significance of
> pairwise alignments, such as the -rand option in gcg.  It is possible,
> of course, to do each step (shuffling one sequence, aligning, and
> calculating the mean and standard deviation) separately.  However, for
> users that don't know how to program, this isn't simple.
>
> Thank you,
> Gila.
>



From ame at esbs.u-strasbg.fr  Wed Dec  3 15:22:07 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Wed, 3 Dec 2003 16:22:07 +0100
Subject: [EMBOSS] remap and GCG mapplot
In-Reply-To: <3FCDE04E.000011.77674@ns.interchange.ca>
References: <3FCDE04E.000011.77674@ns.interchange.ca>
Message-ID: <74EAFDAC-25A4-11D8-AE7F-0005024329A7@esbs.u-strasbg.fr>

It looks good, but I tried to compiled it with MacOSX 10.3 and I got a 
lot of errors...

Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :

> The program TACG ( http://tacg.sourceforge.net/) can substitute for
> some of the GCG applications missing in EMBOSS. Like
>
> mapplot (tacg -l -s )
> map (tacg -T3,1 -sL )
> mapsort (tacg -cF2 )
> mapgel (tacg -g10 -s )
> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>
> Stefanie
>
>> Hello,
>>
>> I am writing for a request for emboss. It would be great that
>> emboss could integrate something similar to the very useful (my
>> point of view) GCG's program MAPPLOT (a graphical representation
>> of a restriction map). I am sure that could be easily added to
>> emboss's remap or restrict.
>> With this feature added I would definitively not use anymore GCG.
>> Any idea. Thanks for the great job.
>> Jean-Christophe
>>
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>>
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
>
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From mad at biol.unlp.edu.ar  Thu Dec  4 00:01:19 2003
From: mad at biol.unlp.edu.ar (=?ISO-8859-1?B?TWFydO1uIFNhcmFjaHU=?=)
Date: Wed,  3 Dec 2003 21:01:19 -0300
Subject: [EMBOSS] MFOLD
In-Reply-To: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>
References: <Pine.SGI.4.05.10312031432150.909178-100000@www.ccmb.res.in>
Message-ID: <1070496079.3fce794f04abb@www.biol.unlp.edu.ar>

At BEN (Belgian EMBnet Node) they are developing a wrapper to use mfold within 
EMBOSS, but I don't know if it is ready for distribution.

Regards,

martin

Quoting Shrish Tiwari <shrish at ccmb.res.in>:

> Hi!
> 
> Is it possible to include MFOLD, for computing DNA/RNA folds into EMBOSS?
> 
> Shrish
> 
> 
> ______________________________________________________________________
> Dr. Shrish Tiwari
> BIC, Centre for Cellular and Molecular Biology
> Uppal Road, Hyderabad - 500 007
> Phone: 91-40-7192776 (work), 91-40-7156603 (home)
> email: shrish at ccmb.res.in
> ______________________________________________________________________
> 


-- 
Mart?n Sarachu
mad at biol.unlp.edu.ar
EMBnet Argentina
http://www.ar.embnet.org


From stefanielager at fastmail.ca  Thu Dec  4 06:17:43 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 4 Dec 2003 01:17:43 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCED187.00006F.07204@ns.interchange.ca>

I don't know anything about MacOSX, but when I had problems with TACG
on Linux Harry Mangalam sent me the latest TACG version 4.0, which
solved my compilation problems.

Stefanie

> It looks good, but I tried to compiled it with MacOSX 10.3 and I
> got a lot of errors...
> 
> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
> 
>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>> for some of the GCG applications missing in EMBOSS. Like
>> 
>> mapplot (tacg -l -s )
>> map (tacg -T3,1 -sL )
>> mapsort (tacg -cF2 )
>> mapgel (tacg -g10 -s )
>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>> 
>> Stefanie
>> 
>>> Hello,
>>> 
>>> I am writing for a request for emboss. It would be great that
>>> emboss could integrate something similar to the very useful (my
>>> point of view) GCG's program MAPPLOT (a graphical representation
>>> of a restriction map). I am sure that could be easily added to
>>> emboss's remap or restrict.
>>> With this feature added I would definitively not use anymore
>>> GCG. Any idea. Thanks for the great job.
>>> Jean-Christophe
>>> 
>>> ________________________
>>> Jean-Christophe Am?, PhD
>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>>> Structurale
>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>> P?le API
>>> Parc d'innovation, Boulevard S?bastien Brant
>>> BP 10413
>>> 67412 ILLKIRCH CEDEX
>>> France
>>> 
>>> tel.: 33 3 90 24 47 05
>>> Fax.: 33 3 90 24 46 86
>> 
>> _________________________________________________________________
>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
> ________________________
> Jean-Christophe Am?, PhD
> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
> Structurale
> ?cole Sup?rieure de Biotechnologie de Strasbourg
> P?le API
> Parc d'innovation, Boulevard S?bastien Brant
> BP 10413
> 67412 ILLKIRCH CEDEX
> France
> 
> tel.: 33 3 90 24 47 05
> Fax.: 33 3 90 24 46 86

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From stefanielager at fastmail.ca  Thu Dec  4 10:25:14 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Thu, 4 Dec 2003 05:25:14 -0500 (EST)
Subject: [EMBOSS] remap and GCG mapplot
Message-ID: <3FCF0B8A.0000F7.07220@ns.interchange.ca>

The "Changelog" of TACG 4.0 says that it has been built on Solaris 5.8
(gcc) and on Mac OSX 10.2 .

Stefanie

"Change Log for tacg development

$Id: ChangeLog,v 1.1.1.1 2001/11/14 18:36:33 mangalam Exp $ 

2003.05.30 Harry Mangalam, hjm at tacgi.com 
 * fixed the ghostscript bug - still some problems in the generation
of the 
   postscript - not enuf error checking, but the thang executes as
it's supposed 
   toat least if the postscript is good.

2003.05.29 Harry Mangalam, hjm at tacgi.com 
 * minor fix to seqio.c to allow OSX to include <dirent.h>
 * removed fmax() declaration - there was no parallel function anyway - 
   looked like the floating point match to imax() but no code for it.
 * Fixed a bunch of stuff in the configure /make process so things don't 
   break on different platforms
 * updated the config.guess & config.sub to allow finding OSX
 * re-included getopt1.c so that it compiles on Solaris - otherwise 
   getopt_long doesn't get defined.
 * added the psprolog file to the tarball so --ps, --pdf can work.
 * added automatic making of newdist and tarball to automagically
build a distro -
   this now works very well and keeps track of the key files to include.
 * tested build procedure on sf compile farm on the following machines:
 
   - Debian 2.2 Intel SMP (gcc 2.95)
     Linux usf-cf-x86-linux-1 2.4.19 #1 SMP  i686 unknown
   
   - RedHat 7.3 Intel SMP (gcc 2.96)
     Linux usf-cf-x86-linux-2.cf.sourceforge.net 2.4.18-5smp #1 SMP \
     i686 unknown
   
   - Debian 3.0  Alpha (gcc 2.95.4)
     Linux usf-cf-alpha-linux-1 2.2.20 #2 alpha unknown
     
   - Debian SPARC (gcc 2.95)
     Linux usf-cf-sparc-linux-1 2.4.18 #2  sparc64 unknown
     
   - Solaris 5.8 (gcc )
      
   - Mac OSX 10.2 (gcc 3.1)
     Darwin ucf-cf-ppc-macosx-2 6.5 Darwin Kernel Version 6.5:  \
     root:xnu/xnu-344.32.obj~1/RELEASE_PPC  Power Macintosh powerpc
   

2003.05.19 Harry Mangalam, hjm at tacgi.com 
 * changed --idonly to have default as 1 (don't have to specify the
flag value)
 

2003.05.16 Harry Mangalam, hjm at tacgi.com 
 * tested vs the old readseq test sequences - seems to read all but
   test.m-paup and test.strider (ascii format).  Have to verify a 
   bit more and see what' not working.  Since I have the binary 
   strider format reader working - it might be useful to mod seqio 
   to do that as well using pcre.
 * fixed a BUG that filtered teh wrong enzyme (filtered on proto 
   index instead of proto[index])
 * added and cleaned up verbosity levels so that verbosity is 
   upwardly inclusive (ie -V3 contains all the verbosity of V1 and V2)
 * make install, make newdist, make tarball, make install_web added to
   Makefile.in and they seem to work altho install_web just tells the 
   user what to do - edit & run the web installer script.

2003.05.09 Harry Mangalam, hjm at tacgi.com 
 * removed all traces of udping.c and udp reporting from code.
 
2003.03.14 Harry Mangalam, hjm at tacgi.com  
 * RE contains .E_olap which is the size of the overlap,
   if any.  Could  be combined with -o to provide selection of REs
   that provide only 5' overhangs  of size 3, for example. currently
   -o5, -o0 -o3; could graft on a hack to allow  user to extend to
   add a number if 5 or 3 ie -o5,5 which would select only REs  that
   have a 5' overhang of length 5 - OK!  Done!


2003.02.25.23 Harry Mangalam, hjm at tacgi.com 
 * 2.25.03 - Brian Frist sez following work on both Linux and SOlaris:
   Fasta EMBL Genbank IG Plain NBRF Phylip3.2 Phylip MSF but there are
some 
   others that fail mysteriously on some platforms - not completely
solved yet..
 * Following worked on Linux but not on SOlaris:
   Phylip3.2 Phylip MSF

 * Following worked on Solaris but not on Linux:
   CODATA

 * and NONE of the other formats generated by readseq worked on either, 
   not even GCG
   This disagrees with running the test sequences from readseq thru it
tho..
   requires more investigation...

   
2002-11.23 Harry Mangalam, hjm at tacgi.com 
  * added code to add a '-' to site numbers when nonpals are found on the
    bottom strand (suggested by Stefanie Lager), so that Site output now
    includes both positive and negative numbers (all numbered relative
to the
    top strand tho).  Still need to add a mod to -S flag to optionally
enable 
    this, tho.
  * added and modified code to allow pattern labels longer than 10
chars - 
    now have to be #defined for building in tacg.h (MAX_PAT_NAME_LEN) and 
    then the RE struct is checked for the longest name and that length is 
    used for output, etc (stored in F.MaxPatNameLen).

2001-10-17 Harry Mangalam, hjm at tacgi.com 
   * Fixed BAD realloc bug in ReadEnz in which test for end of
alloc'ed mem in
      RE was  calculated wrong - basic math error.  Showed up bc
trying to do a
      bunch of matching with errors and the cal overflowed the end of RE.

2001-06-09 Harry Mangalam, hjm at tacgi.com  
  * Added & deleted a bunch of files from CVS to bring things up to date
  * made the Logging of Degens optional to save memory
  * brought tacg.1 man page more up to date.
  * "

> I had no success on Solaris and FreeBSD.
> So on what system should the version 3.5 compile ?
> Do you have any information from the author why the current
> version 4 is not available from sourceforge ?
> 
> Cheers,
> David.
> 
> 
> I don't know anything about MacOSX, but when I had problems with
> TACG on Linux Harry Mangalam sent me the latest TACG version 4.0,
> which solved my compilation problems.
> 
> Stefanie
> 
>> It looks good, but I tried to compiled it with MacOSX 10.3 and I
>> got a lot of errors...
>> 
>> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
>> 
>>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>>> for some of the GCG applications missing in EMBOSS. Like
>>> 
>>> mapplot (tacg -l -s )
>>> map (tacg -T3,1 -sL )
>>> mapsort (tacg -cF2 )
>>> mapgel (tacg -g10 -s )
>>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>>> 
>>> Stefanie
>>> 
>>>> Hello,
>>>> 
>>>> I am writing for a request for emboss. It would be great that
>>>> emboss could integrate something similar to the very useful (my
>>>> point of view) GCG's program MAPPLOT (a graphical
>>>> representation of a restriction map). I am sure that could be
>>>> easily added to emboss's remap or restrict.
>>>> With this feature added I would definitively not use anymore
>>>> GCG. Any idea. Thanks for the great job.
>>>> Jean-Christophe
>>>> 
>>>> ________________________
>>>> Jean-Christophe Am?, PhD
>>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire
>>>> et Structurale
>>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>>> P?le API
>>>> Parc d'innovation, Boulevard S?bastien Brant
>>>> BP 10413
>>>> 67412 ILLKIRCH CEDEX
>>>> France
>>>> 
>>>> tel.: 33 3 90 24 47 05
>>>> Fax.: 33 3 90 24 46 86
>>> 
>>> ________________________________________________________________
>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>> 
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
> 
> _________________________________________________________________
> http://fastmail.ca/ - Fast Secure Web Email for Canadians
> 
> 

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From ame at esbs.u-strasbg.fr  Thu Dec  4 13:12:32 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Thu, 4 Dec 2003 14:12:32 +0100
Subject: [EMBOSS] remap and GCG mapplot
In-Reply-To: <3FCED187.00006F.07204@ns.interchange.ca>
References: <3FCED187.00006F.07204@ns.interchange.ca>
Message-ID: <84DB65C7-265B-11D8-B80D-0005024329A7@esbs.u-strasbg.fr>

Thanks for the information. I wrote to him to ask him TACG version 4 
which I think will very likely also solve my problems.
Jean-Christophe


Le 4 d?c. 03, ? 07:17, Stefanie Lager a ?crit :

> I don't know anything about MacOSX, but when I had problems with TACG
> on Linux Harry Mangalam sent me the latest TACG version 4.0, which
> solved my compilation problems.
>
> Stefanie
>
>> It looks good, but I tried to compiled it with MacOSX 10.3 and I
>> got a lot of errors...
>>
>> Le 3 d?c. 03, ? 14:08, Stefanie Lager a ?crit :
>>
>>> The program TACG ( http://tacg.sourceforge.net/) can substitute
>>> for some of the GCG applications missing in EMBOSS. Like
>>>
>>> mapplot (tacg -l -s )
>>> map (tacg -T3,1 -sL )
>>> mapsort (tacg -cF2 )
>>> mapgel (tacg -g10 -s )
>>> findpatterns (tacg -S2 -R 'path/to/a/pattern/file )
>>>
>>> Stefanie
>>>
>>>> Hello,
>>>>
>>>> I am writing for a request for emboss. It would be great that
>>>> emboss could integrate something similar to the very useful (my
>>>> point of view) GCG's program MAPPLOT (a graphical representation
>>>> of a restriction map). I am sure that could be easily added to
>>>> emboss's remap or restrict.
>>>> With this feature added I would definitively not use anymore
>>>> GCG. Any idea. Thanks for the great job.
>>>> Jean-Christophe
>>>>
>>>> ________________________
>>>> Jean-Christophe Am?, PhD
>>>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>>>> Structurale
>>>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>>>> P?le API
>>>> Parc d'innovation, Boulevard S?bastien Brant
>>>> BP 10413
>>>> 67412 ILLKIRCH CEDEX
>>>> France
>>>>
>>>> tel.: 33 3 90 24 47 05
>>>> Fax.: 33 3 90 24 46 86
>>>
>>> _________________________________________________________________
>>> http://fastmail.ca/ - Fast Secure Web Email for Canadians
>> ________________________
>> Jean-Christophe Am?, PhD
>> U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et
>> Structurale
>> ?cole Sup?rieure de Biotechnologie de Strasbourg
>> P?le API
>> Parc d'innovation, Boulevard S?bastien Brant
>> BP 10413
>> 67412 ILLKIRCH CEDEX
>> France
>>
>> tel.: 33 3 90 24 47 05
>> Fax.: 33 3 90 24 46 86
>
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From louis at gtptech.com  Thu Dec  4 15:28:54 2003
From: louis at gtptech.com (Carole Louis)
Date: 04 Dec 2003 16:28:54 +0100
Subject: [EMBOSS] problem in my program
Message-ID: <1070551736.1392.49.camel@thym>

Hi,

I'm programming in EMBOSS 2.7.1 (not yet in EMBOSS 2.8.0) and I don't
understand why my program does not work. I'm looking for the error since
yesterday but I don't find it. The part of my program where is the
problem is :

      // obtention fin extremite terminale oligo gche
      // mise sequence1 dans tableau
      iterSeq1 = ajStrIter(res2->sequenceGche);
      while (!ajStrIterDone(iterSeq1))
       	{
	          c = ajStrIterGetK(iterSeq1);
	          tabSeq1[i] = c;
	 	        i++;
	 	        ajStrIterNext(iterSeq1);
	        }
      
      // Nucleotide extremite 3' de l'oligo gauche
      Nuc3OligGche = tabSeq1[lenSeq1-1];
      
  
      // obtention fin extremite terminale oligo dte 
      // sequence2 dans tableau
      iterSeq2 = ajStrIter(res2->sequenceDte);
      while (!ajStrIterDone(iterSeq2))
            	{
	              d = ajStrIterGetK(iterSeq2);
	              tabSeq2[j] = d;
	              j++;
	             ajStrIterNext(iterSeq2);
	             }
      
      
      // Nucleotide extremite 3' de l'oligo droite
      Nuc3OligDte = tabSeq2[lenSeq2-1];
   
      ajStrAssCI(&charT, "T",1);
      ajStrAssCI(&charA, "A",1);
           
      if ((ajStrMatchCaseC (charA,&Nuc3OligGche))||(ajStrMatchCaseC
(charT,&Nuc3OligGche)))
      	{
	        ajFmtPrintF(outf, "oligo gche finit par A ou T \n");
	        res2->score = res2->score - 1; 
      	}
      
      if ((ajStrMatchCaseC (charAbis,&Nuc3OligDte))||(ajStrMatchCaseC
(charTbis,&Nuc3OligDte)))
      	{
	        ajFmtPrintF(outf, "oligo dte finit par A ou T \n");
	        res2->score = res2->score - 1; 
      	}
 
There isn't any problem with the first buckle 1 (see in red) but my
program does'nt go is the buckle 2 (see in green) as it should do it and
as it do with the buckle 1.  Is someone can help me, please. I have no
more idea now and don't know what to do. May be my problem will appear
very clear for someone. I hope it, in fact.      :-) 
Thanks,
Carole Louis

        
  
	  



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From gtps5 at gtptech.com  Thu Dec  4 15:45:45 2003
From: gtps5 at gtptech.com (Carole Louis)
Date: 04 Dec 2003 16:45:45 +0100
Subject: [EMBOSS] problem in my program
In-Reply-To: <1070551736.1392.49.camel@thym>
References: <1070551736.1392.49.camel@thym>
Message-ID: <1070552752.1435.53.camel@thym>

I read my mail and I saw I made a mistake copying my program but I
change it and it 'is the good version below.

Le jeu 04/12/2003 ? 16:28, Carole Louis a ?crit :

    Hi, 
    
    I'm programming in EMBOSS 2.7.1 (not yet in EMBOSS 2.8.0) and I
    don't understand why my program does not work. I'm looking for the
    error since yesterday but I don't find it. The part of my program
    where is the problem is : 
    
          // obtention fin extremite terminale oligo gche
          // mise sequence1 dans tableau
          iterSeq1 = ajStrIter(res2->sequenceGche);
          while (!ajStrIterDone(iterSeq1))
           {
              c = ajStrIterGetK(iterSeq1);
              tabSeq1[i] = c;
            i++;
            ajStrIterNext(iterSeq1);
            }
          
          // Nucleotide extremite 3' de l'oligo gauche
          Nuc3OligGche = tabSeq1[lenSeq1-1];
          
      
          // obtention fin extremite terminale oligo dte 
          // sequence2 dans tableau
          iterSeq2 = ajStrIter(res2->sequenceDte);
          while (!ajStrIterDone(iterSeq2))
                {
                  d = ajStrIterGetK(iterSeq2);
                  tabSeq2[j] = d;
                  j++;
                 ajStrIterNext(iterSeq2);
                 }
          
          
          // Nucleotide extremite 3' de l'oligo droite
          Nuc3OligDte = tabSeq2[lenSeq2-1];
       
          ajStrAssCI(&charT, "T",1);
          ajStrAssCI(&charA, "A",1);
               
          if ((ajStrMatchCaseC (charA,&Nuc3OligGche))||(ajStrMatchCaseC
    (charT,&Nuc3OligGche)))
          {
            ajFmtPrintF(outf, "oligo gche finit par A ou T \n");
            res2->score = res2->score - 1; 
          }
          
          if ((ajStrMatchCaseC (charA,&Nuc3OligDte))||(ajStrMatchCaseC
    (charT,&Nuc3OligDte)))
          {
            ajFmtPrintF(outf, "oligo dte finit par A ou T \n");
            res2->score = res2->score - 1; 
          }
    
    There isn't any problem with the first buckle 1 (see in red) but my
    program does'nt go is the buckle 2 (see in green) as it should do it
    and as it do with the buckle 1.  Is someone can help me, please. I
    have no more idea now and don't know what to do. May be my problem
    will appear very clear for someone. I hope it, in fact.      :-) 
    Thanks, 
    Carole Louis 
    
            
      
      
    
    
    
    
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From gbottu at ben.vub.ac.be  Thu Dec  4 18:58:28 2003
From: gbottu at ben.vub.ac.be (Guy Bottu)
Date: Thu, 4 Dec 2003 19:58:28 +0100
Subject: [EMBOSS] gap penalties for water
In-Reply-To: <3FCDF797.8020309@md.huji.ac.il>
References: <3FCDF797.8020309@md.huji.ac.il>
Message-ID: <20031204185828.GA11119@bigben.ulb.ac.be>


Well, there are two ways to compute a penalty for a gap of n positions :

<gap opening penalty> + (n - 1) * <gap extension penalty>
<gap penalty> + n * <gap length penalty>

The first way is used by EMBOSS and BLAST
The second way is used by GCG, Staden and CLUSTAL
fastA used for a long time the first way, but Prof. pearson decided 
recently to shift to the second

The two methods are basically equivalent (it depends on which values you 
choose) and you can discuss at infinitam and ad nauseam which is best.

	Regards,
	Guy Bottu
	Belgian EMBnet Node


From news at venturereporter.net  Wed Dec 10 19:01:38 2003
From: news at venturereporter.net (Venture Reporter)
Date: 10 Dec 2003 19:01:38 -0000
Subject: [EMBOSS] Venture Reporter Research: Two Biotech reports for only $395!
Message-ID: <20031210190138.26888.qmail@sfq4.venturereporter.net>

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From American_Biotechnology_Laboratory at xmr3.com  Thu Dec 11 16:52:00 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Thu, 11 Dec 2003 11:52:00 -0500
Subject: [EMBOSS] Laboratory Scientific Product Expo
Message-ID: <I-0-757640-19599867-2-9499-US2-E2B7AA44@xmr3.com>

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From American_Laboratory at xmr3.com  Thu Dec 11 16:57:15 2003
From: American_Laboratory at xmr3.com (American Laboratory)
Date: Thu, 11 Dec 2003 11:57:15 -0500
Subject: [EMBOSS] Laboratory Scientific Product Expo
Message-ID: <I-2-757641-19599724-2-27942-US2-E6FB86D2@xmr3.com>

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From OBJ at obj.org  Fri Dec 12 00:09:40 2003
From: OBJ at obj.org (OBJ)
Date: Fri, 12 Dec 2003 00:09:40 +0000
Subject: [EMBOSS] No minimo, =?ISO-8859-1?Q?d=EA?= o beneficio da
 =?ISO-8859-1?Q?d=FAvida!?=
Message-ID: <20031212000945.8760A7D6FE@mercury.hgmp.mrc.ac.uk>


Boas, antes de mais gostaria de informar que o seu email foi retirado de uma ou mais p?ginas
da Internet e que este seu email ser? apagado, logo ap?s o envio desta mensagem.

O que me faz enviar esta mensagem, ? muio simples, tenho estado a desenvolver um neg?cio independente
a partir de casa no ?ltmos 9 meses, o qual j? conhecia ? mais de 10 anos, mas s? h? 9 meses tive a
curiosidade e motivo para o analizar. Como podem entender abraceio-o e, gostaria de lhe dar a conhecer
esta oportunidade. Se por qualquer motivo os seus sonhos de estilo de vida lhe parecem cada vez
mais longinquos, se por algum motivo acha que, independentemente da sua idade, nunca os vai conseguir
alcan?ar, gostaria de lhe poder dar a analizar esta oportunidade.

Quantos de n?s trabalha-mos um vida inteira para construir algo e chega-mos ao fim da vida sem ter nada
ou tendo apenas uma parte muito pequena daquilo que ambiciona-mos.

Gostaria de lhe perguntar se estaria disposto(a), a apenas com algumas horas por semana, e fazendo um sacrificio e
esfor?o extra, durante os pr?ximo 3 a 4 anos, dedicar essas horas por semana e da? fazer crescer um
rendimento tal que n?o se teria de preocupar com a sua vida fincanceira.

O que me diz a poder ganhar 500? extra, juntando ao dinheiro que j? ganha, e fazer com que estes 500?
crescam de m?s pra m?s a uma velocidade impressionante. Estaria disposto a fazer esse esfor?o?

Se esta no minimo curioso para analizar esta oportunidade, ent?o contacte-me de forma a poder assitir
via internet a uma apresenta??o no conforto da sua casa, e talvez, quem sabe, come?ar a mudar algo na sua vida.

Fernanda Manuela
as1531033 at sapo.pt


From jack.leunissen at wur.nl  Fri Dec 12 12:07:37 2003
From: jack.leunissen at wur.nl (Jack Leunissen)
Date: Fri, 12 Dec 2003 13:07:37 +0100
Subject: [EMBOSS] restrict -alphabetic
Message-ID: <000601c3c0a8$8bd8b620$d930e089@bioinf01>

Dear EMBOSS gurus,
 
I don't understand the output of the RESTRICT program when using the
-ALPHABETIC option. The output is more or less alphabetically sorted,
but not completely. So the question remains: sorted alphabetically on
what?
 
Cheers,
Jack
 
 
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From American_Biotechnology_Laboratory at xmr3.com  Mon Dec 15 19:01:49 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Mon, 15 Dec 2003 14:01:49 -0500
Subject: [EMBOSS] ALA LabFusion 2004 Call for Papers
Message-ID: <I-8-757640-19670149-2-9499-US2-6577A7C6@xmr3.com>

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From brett.kaufman at mcgill.ca  Mon Dec 15 20:48:53 2003
From: brett.kaufman at mcgill.ca (Brett Kaufman)
Date: Mon, 15 Dec 2003 15:48:53 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
Message-ID: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca>

I have receive such fantastic and patient help from Tim Carver that I 
though I would submit experience back to the emboss boards.

standalone Jemboss EMBOSS-2.8.0 successfully installed:

All of this was done on 10.3.1 with the latest fink installed and 
working.  At the time, EMBOSS-2.8.0 wasn't available through fink, so 
it was downloaded and installed from command line.  To repeat my steps, 
you will need to be certain that libiconv, gd2, and libpng are current. 
Remember to run fink selfupdate and update all a time or two to be 
certain everything is completely there ;).

download emboss-2.8.0, and embassy components. Emboss will install in 
/usr/local, so I moved the downloaded folders to a new directory 
/usr/local/installers.  The original folder is needed after the 
install, so this make a permanent home for the EMBOSS-2.8.0 folder.  
gunzip and tar-xvf everything.

 >cd /usr/local/installers/EMBOSS-2.8.0/jemboss/utils
 >./install-jemboss-server.sh

The Java file for Panther is:
/System/Library/Frameworks/JavaVM.framework/Home

Accepting the default responses usually works, except for the png 
driver.  In this installation, use --with-pngdriver=/sw.

when prompted, move the decompressed embassy files to the new embassy 
folder in EMBOSS-2.8.0 within the installer.

when installation is finished, there a few things that are worth 
changing.

As panther uses bash, I used pico ~/.bashrc to make sure that I can run 
emboss  from any directory):
PATH=$PATH:/usr/local/emboss/bin

The runJemboss file needs to be modified; however, the prescribed 
modification on the web are for runJemboss.csh, which is from 
emboss-2.7.1, rather than runJemboss.sh, which you will be using.

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

remove the # on DYLD_LIBRARY_PATH...

Keep an eye open for word wrap issues.  Should you have launch issues, 
try pico -w and look for disconnect text.

I added Jemboss to the X11 menu:
Applications -> Customize
Name= Jemboss
Command= /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh
Shortcut=j
done

hitting command-j will launch the application if x11 is active.

Make sure to dl clustalw and install it in /usr/local/bin to get emma 
to work properly.

primer3: this is sort of ugly, but it works.
download primer3_0_9_test from the whitehead institute. gunzip and tar 
-xvf, then move to installers.
 >cd /usr/local/installers/primer3_0_9_test/src

I had to edit the Makefile using a hint from Alex Brown.
I removed the line:
LIBOPTS ='-static'
and then removed all references to $(LIBOPTS)

It has been suggested that you change CC=gcc to CC=CC, but I haven't.
 >make primer3
when finished, you can test
 >cd ../test
 >./primer_test.pl
Don't be totally dismayed if you see a FAILED during test after primer 
comparison.
if you ran the test, then
 >cd ../src
you need the primer3_core in the path of emboss, so copy it to 
emboss/bin
 >cp primer3_core /usr/local/emboss/bin
Seems to work for me from command line or Jemboss.  Let me know if this 
hack didn't cut it for you!

at this point it might be useful to build you locate database:
 >sudo /usr/libexec/locate.updatedb

Activating all the goodies:
you need to run:
aaextractindex, cutgextract, printsextract, prosextract, rebase
(there may be others that I ran, or other that I have yet to discover 
that I need to run).  I did this from commandline, but it looks like 
Jemboss will run them also.  Some of the target databases are in 
/usr/local/installers/EMBOSS-2.8.0/test/data, others have to be 
downloaded.  The appropriate source is on the corresponding help pages.




Current problems:
I have an display issue with .png files.  Plots and graphs made 
correctly, but they do not display properly in the results window.  If 
I save those displayed results, and open them in preview, they are 
fine; thus, it is a display issue only.

I hope this adequately thorough to provide some clues to any problems 
you are having with your install.

-Brett


????????????????????????????????????????????????????????
Brett Kaufman, Ph.D
3801 University
Rm 676
Montreal, QC H3A 2B4
Canada

brett.kaufman at mcgill.ca
(514) 398 8523
(514) 398 1509 (fax)
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From hsut5 at yahoo.com  Tue Dec 16 01:08:25 2003
From: hsut5 at yahoo.com (Tai Hsu)
Date: Mon, 15 Dec 2003 17:08:25 -0800 (PST)
Subject: [EMBOSS] suggestion of a new application
Message-ID: <20031216010825.55889.qmail@web20810.mail.yahoo.com>

Dear Sirs:

I like to offer a string alignment utility that have the advantages of
both of the "local alignement" and the "global alignment", and none of
their disadvantages. It's called Walking Tree method. Please let me
know how I can submit my offer.

Thanks,
Tai Hsu, Ph.D.

__________________________________
Do you Yahoo!?
New Yahoo! Photos - easier uploading and sharing.
http://photos.yahoo.com/


From brettkaufman at videotron.ca  Tue Dec 16 01:37:50 2003
From: brettkaufman at videotron.ca (Brett Kaufman)
Date: Mon, 15 Dec 2003 20:37:50 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
In-Reply-To: <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net>
References: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca> <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net>
Message-ID: <757B5350-2F68-11D8-AD83-000A95DA5C82@videotron.ca>

Koen,
Have you compiled Jemboss from the finkinstall?  Have you considered 
making a jemboss package for fink?

-Brett

On 15-Dec-03, at 7:59 PM, Koen van der Drift wrote:

> On Dec 15, 2003, at 3:48 PM, Brett Kaufman wrote:
>
>> All of this was done on 10.3.1 with the latest fink installed and 
>> working.  At the time, EMBOSS-2.8.0 wasn't available through fink,
>
> As the maintainer of EMBOSS I can inform you that 2.8.0 is now 
> available through fink (unstable tree).
>
> - Koen.
>



From kvddrift at earthlink.net  Tue Dec 16 01:39:30 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Mon, 15 Dec 2003 20:39:30 -0500
Subject: [EMBOSS] Standalone on MacOSX Panther success
In-Reply-To: <6DFCEB9C-2F66-11D8-AD83-000A95DA5C82@mcgill.ca>
References: <180B07C6-2F40-11D8-BC28-000A95DA5C82@mcgill.ca> <09F2BDD2-2F63-11D8-9B0B-003065A5FDCC@earthlink.net> <6DFCEB9C-2F66-11D8-AD83-000A95DA5C82@mcgill.ca>
Message-ID: <B10A997E-2F68-11D8-9B0B-003065A5FDCC@earthlink.net>


On Dec 15, 2003, at 8:23 PM, Brett Kaufman wrote:

> Have you compiled Jemboss from the finkinstall?  Have you considered 
> making a jemboss package for fink?
>

So far, 'no' to both questions. I use emboss-kaptain (also from fink) 
as a GUI.

- Koen.



From American_Biotechnology_Laboratory at xmr3.com  Tue Dec 16 14:31:25 2003
From: American_Biotechnology_Laboratory at xmr3.com (American Biotechnology Laboratory)
Date: Tue, 16 Dec 2003 09:31:25 -0500
Subject: [EMBOSS] American Biotechnology Laboratory February 2004 
Message-ID: <I-4-757640-19816265-2-9499-US2-D30F19D2@xmr3.com>

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From Caroline.Barretto at rdls.nestle.com  Tue Dec 16 16:11:37 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Tue, 16 Dec 2003 17:11:37 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED50579E@chlsne01.nestle.com>

Dear all,
 
Did anybody notice that the seqret program seems to be limited by the number
of sequences to convert ? I am trying to convert 1 file containing 23000
genbank sequences into GCG format.
Do you have a suggestion for that ?
 
Thank you very much,
 
Regards,
 
Caroline.
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From simon.andrews at bbsrc.ac.uk  Tue Dec 16 16:46:39 2003
From: simon.andrews at bbsrc.ac.uk (simon andrews (BI))
Date: Tue, 16 Dec 2003 16:46:39 -0000
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <2DC41140A89ED411989D00508BDCD9ED01E28C3E@bi-exsrv1.iapc.bbsrc.ac.uk>


-----Original Message-----
From: Barretto,Caroline,LAUSANNE,NRC/BAS [mailto:Caroline.Barretto at rdls.nestle.com] 
Sent: 16 December 2003 16:12
To: emboss at embnet.org
Subject: [EMBOSS] Does seqret have limitations ?


> Dear all,
> 
> Did anybody notice that the seqret program seems to 
> be limited by the number of sequences to convert ? I 
> am trying to convert 1 file containing 23000 genbank 
> sequences into GCG format.
>
> Do you have a suggestion for that ?

Seqret is not limited by number of files.  I routinely pass the whole of EMBL through seqret and it works fine.  What error do you get when seqret stops?  Could it just be that there is a malformed entry part way through your file?

Is the file you are trying to convert >2Gb in size?  If so this could be the reason for the failure rather than seqret being limited by the number of sequences.  In this case though I thought that the failure would happen when the file was first opened and not after a certain number of sequences had passed through.

If the problem is a large file you might be able to get round this by using a pipe to get information into seqret.  Try

cat your_genbank_file.gb | seqret -filter -osf gcg > your_gcg_file.gcg

This should work as long as your OS version of cat and your shell can handle large files.

Hope this helps

Simon.


From Caroline.Barretto at rdls.nestle.com  Tue Dec 16 17:26:53 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Tue, 16 Dec 2003 18:26:53 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED50579F@chlsne01.nestle.com>

Dear Simon,

I don't receive any error from seqret, it simply stops just as if it was
correctly finished. 
The file is not bigger than 2Gb:
$ du -sk file.gbk
74680   file.gbk

Even with the cat command you sent me, I only get 17143 sequences formatted
in GCG format. (it is the same if I try to convert in fasta format)

$ grep -c "Check" file.gcg
17143
$ grep -c "LOCUS" file.gbk
26045

$ seqret file.gbk -osformat fasta -outseq test
Reads and writes (returns) sequences
$ grep -c ">" test
17143

If anybody has an idea...

Thanks a lot,

Caroline.



-----Original Message-----
From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
Sent: mardi, 16. d?cembre 2003 17:47
To: 'emboss at embnet.org'
Subject: RE: [EMBOSS] Does seqret have limitations ?



-----Original Message-----
From: Barretto,Caroline,LAUSANNE,NRC/BAS
[mailto:Caroline.Barretto at rdls.nestle.com] 
Sent: 16 December 2003 16:12
To: emboss at embnet.org
Subject: [EMBOSS] Does seqret have limitations ?


> Dear all,
> 
> Did anybody notice that the seqret program seems to 
> be limited by the number of sequences to convert ? I 
> am trying to convert 1 file containing 23000 genbank 
> sequences into GCG format.
>
> Do you have a suggestion for that ?

Seqret is not limited by number of files.  I routinely pass the whole of
EMBL through seqret and it works fine.  What error do you get when seqret
stops?  Could it just be that there is a malformed entry part way through
your file?

Is the file you are trying to convert >2Gb in size?  If so this could be the
reason for the failure rather than seqret being limited by the number of
sequences.  In this case though I thought that the failure would happen when
the file was first opened and not after a certain number of sequences had
passed through.

If the problem is a large file you might be able to get round this by using
a pipe to get information into seqret.  Try

cat your_genbank_file.gb | seqret -filter -osf gcg > your_gcg_file.gcg

This should work as long as your OS version of cat and your shell can handle
large files.

Hope this helps

Simon.
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From luqiang at scbit.org  Wed Dec 17 02:20:32 2003
From: luqiang at scbit.org (Lu Qiang)
Date: Wed, 17 Dec 2003 10:20:32 +0800
Subject: [EMBOSS] Pepinfo's postscript output
Message-ID: <20031217021745.B5A2E7D790@mercury.hgmp.mrc.ac.uk>

Guys,

When I use pepinfo as following:
pepinfo -inseq PCNA.fasta -graph ps -outfile pepinfo.out
pepinfo.ps is created. However, the two-page graph output could not be showed in GSView. Error is listed as:
DSC Error
EPS files may have 0 or 1 pages. This 'EPS' file has
more than this and so is not an EPS file.
You cannot use 'Print To' ?Encapsulated PostScriptFile' for
print multipage files. The correct method is to connect 
the printer to FILE: or to select 'Print to File'.
..

Could anyone tell me how to process this error, and thus see the 2nd page in the pepinfo.ps?

regards,

Lu Qiang
luqiang at scbit.org
2003-12-17




From stefanielager at fastmail.ca  Wed Dec 17 06:05:56 2003
From: stefanielager at fastmail.ca (Stefanie Lager)
Date: Wed, 17 Dec 2003 01:05:56 -0500 (EST)
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <3FDFF244.000199.02566@ns.interchange.ca>

It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
> 
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
> 
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
> 
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
> 
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
> 
> If anybody has an idea...
> 
> Thanks a lot,
> 
> Caroline.
> 
> 
> 
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
> 
> 
> 
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
> 
> 
>> Dear all,
>> 
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>> 
>> Do you have a suggestion for that ?
> 
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
> 
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
> 
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
> 
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
> 
> This should work as long as your OS version of cat and your shell
> can handle large files.
> 
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians

From David.Bauer at SCHERING.DE  Wed Dec 17 07:44:23 2003
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 17 Dec 2003 08:44:23 +0100
Subject: Antwort: [EMBOSS] Pepinfo's postscript output
Message-ID: <OF56828184.DB77A61A-ONC1256DFF.00297B08@schering.de>


Hi Lu,

which version of GSview are you using? I just tested it with 4.4 (output
from EMBOSS2.8.0).
GSview also complains (correctly) about the second page but it can also
show this page with the hydropathy plots.
Workarounds:
1) tell pepinfo to produce only one graph
2) open pepinfo.ps with a text editor and remove the line with the bounding
box definition.

Hope this helps,
David.


                                                                                                               
                      "Lu Qiang"                                                                               
                      <luqiang at scbit.o                                                                         
                      rg>                      An:      "emboss at embnet.org" <emboss at embnet.org>                
                      Gesendet von:            Kopie:                                                          
                      owner-emboss at hgm         Thema:   [EMBOSS] Pepinfo's postscript output                   
                      p.mrc.ac.uk                                                                              
                                                                                                               
                                                                                                               
                      17.12.03 03:20                                                                           
                                                                                                               
                                                                                                               




Guys,

When I use pepinfo as following:
pepinfo -inseq PCNA.fasta -graph ps -outfile pepinfo.out
pepinfo.ps is created. However, the two-page graph output could not be
showed in GSView. Error is listed as:
DSC Error
EPS files may have 0 or 1 pages. This 'EPS' file has
more than this and so is not an EPS file.
You cannot use 'Print To' ?Encapsulated PostScriptFile' for
print multipage files. The correct method is to connect
the printer to FILE: or to select 'Print to File'.
..

Could anyone tell me how to process this error, and thus see the 2nd page
in the pepinfo.ps?

regards,

Lu Qiang
luqiang at scbit.org
2003-12-17






From David.Bauer at SCHERING.DE  Wed Dec 17 07:58:36 2003
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Wed, 17 Dec 2003 08:58:36 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <OFD262E18F.1898DE09-ONC1256DFF.002AAF88@schering.de>


Another explanation could be if there is a Contig type entry in the GenBank
File.
The Contig GenBank entries do not contain any sequence. The feature table
contains only references to other sequence entries.
Seqret can not handle this type of virtual sequence entries.

David.


                                                                                                               
                      "Stefanie Lager"                                                                         
                      <stefanielager at f                                                                         
                      astmail.ca>              An:      emboss at embnet.org                                      
                      Gesendet von:            Kopie:                                                          
                      owner-emboss at hgm         Thema:   RE: [EMBOSS] Does seqret have limitations ?            
                      p.mrc.ac.uk                                                                              
                                                                                                               
                                                                                                               
                      17.12.03 07:05                                                                           
                                                                                                               
                                                                                                               




It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
>
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
>
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
>
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
>
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
>
> If anybody has an idea...
>
> Thanks a lot,
>
> Caroline.
>
>
>
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
>
>
>
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
>
>
>> Dear all,
>>
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>>
>> Do you have a suggestion for that ?
>
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
>
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
>
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
>
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
>
> This should work as long as your OS version of cat and your shell
> can handle large files.
>
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians






From Caroline.Barretto at rdls.nestle.com  Wed Dec 17 10:27:39 2003
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Wed, 17 Dec 2003 11:27:39 +0100
Subject: [EMBOSS] Does seqret have limitations ?
Message-ID: <EF9E44B0F76FDB4396B9EF18A66545ED021E351F@chlsne01.nestle.com>

Thank you very much to everybody, the problem was, as some of you suspected,
in the genbank file...

Best wishes

Caroline.

 

                      "Stefanie Lager"

                      <stefanielager at f

                      astmail.ca>              An:      emboss at embnet.org

                      Gesendet von:            Kopie:

                      owner-emboss at hgm         Thema:   RE: [EMBOSS] Does
seqret have limitations ?            
                      p.mrc.ac.uk

 

 

                      17.12.03 07:05

 

 





It sounds as if it's problems with a single sequence in the file. Try
removing the sequence it hangs on or try split the original file in
parts and see if it there is a single sequence it hangs on. Other
programs can have problems with end of line characters, but this
doesn't sound like that.

Stefanie

> Dear Simon,
>
> I don't receive any error from seqret, it simply stops just as if
> it was correctly finished.
> The file is not bigger than 2Gb:
> $ du -sk file.gbk
> 74680   file.gbk
>
> Even with the cat command you sent me, I only get 17143 sequences
> formatted in GCG format. (it is the same if I try to convert in
> fasta format)
>
> $ grep -c "Check" file.gcg
> 17143
> $ grep -c "LOCUS" file.gbk
> 26045
>
> $ seqret file.gbk -osformat fasta -outseq test
> Reads and writes (returns) sequences
> $ grep -c ">" test
> 17143
>
> If anybody has an idea...
>
> Thanks a lot,
>
> Caroline.
>
>
>
> -----Original Message-----
> From: simon andrews (BI) [mailto:simon.andrews at bbsrc.ac.uk]
> Sent: mardi, 16. d?cembre 2003 17:47
> To: 'emboss at embnet.org'
> Subject: RE: [EMBOSS] Does seqret have limitations ?
>
>
>
> -----Original Message-----
> From: Barretto,Caroline,LAUSANNE,NRC/BAS
> [mailto:Caroline.Barretto at rdls.nestle.com]
> Sent: 16 December 2003 16:12
> To: emboss at embnet.org
> Subject: [EMBOSS] Does seqret have limitations ?
>
>
>> Dear all,
>>
>> Did anybody notice that the seqret program seems to
>> be limited by the number of sequences to convert ? I
>> am trying to convert 1 file containing 23000 genbank
>> sequences into GCG format.
>>
>> Do you have a suggestion for that ?
>
> Seqret is not limited by number of files.  I routinely pass the
> whole of EMBL through seqret and it works fine.  What error do you
> get when seqret stops?  Could it just be that there is a malformed
> entry part way through your file?
>
> Is the file you are trying to convert >2Gb in size?  If so this
> could be the reason for the failure rather than seqret being
> limited by the number of sequences.  In this case though I thought
> that the failure would happen when the file was first opened and
> not after a certain number of sequences had passed through.
>
> If the problem is a large file you might be able to get round this
> by using a pipe to get information into seqret.  Try
>
> cat your_genbank_file.gb | seqret -filter -osf gcg >
> your_gcg_file.gcg
>
> This should work as long as your OS version of cat and your shell
> can handle large files.
>
> Hope this helps

_________________________________________________________________
    http://fastmail.ca/ - Fast Secure Web Email for Canadians



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From georg.otto at tuebingen.mpg.de  Thu Dec 18 16:18:25 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Thu, 18 Dec 2003 17:18:25 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
Message-ID: <web-7083690@tuebingen.mpg.de>

Hi,

I tried to compile EMBOSS on a new computer running Mac OSX
10.3 unfortunately, the compile process aborts with the
error message:

/bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
 aaindexextract.o ../nucleus/libnucleus.la
../ajax/libajaxg.la ../ajax/libajax.la
../plplot/libplplot.la -lX11  -lm 
gcc -O2 -o .libs/aaindexextract aaindexextract.o
 ../nucleus/.libs/libnucleus.dylib
../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
../plplot/.libs/libplplot.dylib -lX11 -lm
ld: can't locate file for: -lX11
make[2]: *** [aaindexextract] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1


As I understand, EMBOSS has problems with Mac?s X11. Is
there any way to get around this.

Any help will be highly appreciated.

Cheers,

Georg

-- 
Georg Wilhelm Otto
Max-Planck-Institute for Developmental Biology
Department 3 - Genetics
Spemannstrasse 35
D-72076 Tuebingen (Germany)
phone:   +49-7071-601393
e-mail: georg.otto at tuebingen.mpg.de


From ame at esbs.u-strasbg.fr  Thu Dec 18 16:51:32 2003
From: ame at esbs.u-strasbg.fr (Jean-Christophe AME)
Date: Thu, 18 Dec 2003 17:51:32 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <web-7083690@tuebingen.mpg.de>
References: <web-7083690@tuebingen.mpg.de>
Message-ID: <6EE19D7E-317A-11D8-8CA7-0005024329A7@esbs.u-strasbg.fr>

Hi Georg,

I have the same configuration and didn't have any problem compiling it. 
You should get from the developer tools CD the X11SDK which is an 
option to install.

My computer is even not supported by panther (a powerbook wallstreet + 
G4 upgrade) and I have no problem with it at all.
Sincerely,
Jean-Christophe


Le 18 d?c. 03, ? 17:18, Georg Otto a ?crit :

> Hi,
>
> I tried to compile EMBOSS on a new computer running Mac OSX
> 10.3 unfortunately, the compile process aborts with the
> error message:
>
> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>  aaindexextract.o ../nucleus/libnucleus.la
> ../ajax/libajaxg.la ../ajax/libajax.la
> ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>  ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
>
> As I understand, EMBOSS has problems with Mac?s X11. Is
> there any way to get around this.
>
> Any help will be highly appreciated.
>
> Cheers,
>
> Georg
>
> -- 
> Georg Wilhelm Otto
> Max-Planck-Institute for Developmental Biology
> Department 3 - Genetics
> Spemannstrasse 35
> D-72076 Tuebingen (Germany)
> phone:   +49-7071-601393
> e-mail: georg.otto at tuebingen.mpg.de
>
>
________________________
Jean-Christophe Am?, PhD
U.P.R. 9003 du CNRS - Canc?rog?n?se et Mutag?n?se Mol?culaire et 
Structurale
?cole Sup?rieure de Biotechnologie de Strasbourg
P?le API
Parc d'innovation, Boulevard S?bastien Brant
BP 10413
67412 ILLKIRCH CEDEX
France

tel.: 33 3 90 24 47 05
Fax.: 33 3 90 24 46 86

http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
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From brettkaufman at videotron.ca  Fri Dec 19 01:35:13 2003
From: brettkaufman at videotron.ca (Brett Kaufman)
Date: Thu, 18 Dec 2003 20:35:13 -0500
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <web-7083690@tuebingen.mpg.de>
References: <web-7083690@tuebingen.mpg.de>
Message-ID: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>

Georg,
How were you installing emboss, from fink or by what method?

Were there errors earlier in the install?

I have emboss running on 10.3, so far, so good.  Have you might need 
full dev tools and x11 sdk.

-Brett
On 18-Dec-03, at 11:18 AM, Georg Otto wrote:

> Hi,
>
> I tried to compile EMBOSS on a new computer running Mac OSX
> 10.3 unfortunately, the compile process aborts with the
> error message:
>
> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>  aaindexextract.o ../nucleus/libnucleus.la
> ../ajax/libajaxg.la ../ajax/libajax.la
> ../plplot/libplplot.la -lX11  -lm
> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>  ../nucleus/.libs/libnucleus.dylib
> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
> ../plplot/.libs/libplplot.dylib -lX11 -lm
> ld: can't locate file for: -lX11
> make[2]: *** [aaindexextract] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
>
> As I understand, EMBOSS has problems with Mac?s X11. Is
> there any way to get around this.
>
> Any help will be highly appreciated.
>
> Cheers,
>
> Georg
>
> -- 
> Georg Wilhelm Otto
> Max-Planck-Institute for Developmental Biology
> Department 3 - Genetics
> Spemannstrasse 35
> D-72076 Tuebingen (Germany)
> phone:   +49-7071-601393
> e-mail: georg.otto at tuebingen.mpg.de
>



From georg.otto at tuebingen.mpg.de  Fri Dec 19 10:47:02 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Fri, 19 Dec 2003 11:47:02 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>
Message-ID: <ADB7FB24-3210-11D8-BF4B-003065C99468@tuebingen.mpg.de>

Dear all,

I think that I could solve the problem of compiling and running EMBOSS 
on Mac OS 10.3, thanks to the help of Jean-Christophe Ame and Alan 
Bleasby. On my Computer, X11 was installed but not X11 SDK. This comes 
as an extra package on the developer CD. I installed it, then i 
configured and compiled EMBOSS (I used the distribution from the EMBOSS 
website, not the fink). It compiled without problems and it runs now.

Cheers,

Georg


On Friday, December 19, 2003, at 02:35 AM, Brett Kaufman wrote:

> Georg,
> How were you installing emboss, from fink or by what method?
>
> Were there errors earlier in the install?
>
> I have emboss running on 10.3, so far, so good.  Have you might need 
> full dev tools and x11 sdk.
>
> -Brett
> On 18-Dec-03, at 11:18 AM, Georg Otto wrote:
>
>> Hi,
>>
>> I tried to compile EMBOSS on a new computer running Mac OSX
>> 10.3 unfortunately, the compile process aborts with the
>> error message:
>>
>> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>>  aaindexextract.o ../nucleus/libnucleus.la
>> ../ajax/libajaxg.la ../ajax/libajax.la
>> ../plplot/libplplot.la -lX11  -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>>  ../nucleus/.libs/libnucleus.dylib
>> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
>> ../plplot/.libs/libplplot.dylib -lX11 -lm
>> ld: can't locate file for: -lX11
>> make[2]: *** [aaindexextract] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>> As I understand, EMBOSS has problems with Mac?s X11. Is
>> there any way to get around this.
>>
>> Any help will be highly appreciated.
>>
>> Cheers,
>>
>> Georg
>>
>> -- 
>> Georg Wilhelm Otto
>> Max-Planck-Institute for Developmental Biology
>> Department 3 - Genetics
>> Spemannstrasse 35
>> D-72076 Tuebingen (Germany)
>> phone:   +49-7071-601393
>> e-mail: georg.otto at tuebingen.mpg.de
>>
>



From georg.otto at tuebingen.mpg.de  Fri Dec 19 10:47:02 2003
From: georg.otto at tuebingen.mpg.de (Georg Otto)
Date: Fri, 19 Dec 2003 11:47:02 +0100
Subject: [EMBOSS] EMBOSS on osx 10.3
In-Reply-To: <97296D2C-31C3-11D8-8823-000A95DA5C82@videotron.ca>
Message-ID: <ADB7FB24-3210-11D8-BF4B-003065C99468@tuebingen.mpg.de>

Dear all,

I think that I could solve the problem of compiling and running EMBOSS 
on Mac OS 10.3, thanks to the help of Jean-Christophe Ame and Alan 
Bleasby. On my Computer, X11 was installed but not X11 SDK. This comes 
as an extra package on the developer CD. I installed it, then i 
configured and compiled EMBOSS (I used the distribution from the EMBOSS 
website, not the fink). It compiled without problems and it runs now.

Cheers,

Georg


On Friday, December 19, 2003, at 02:35 AM, Brett Kaufman wrote:

> Georg,
> How were you installing emboss, from fink or by what method?
>
> Were there errors earlier in the install?
>
> I have emboss running on 10.3, so far, so good.  Have you might need 
> full dev tools and x11 sdk.
>
> -Brett
> On 18-Dec-03, at 11:18 AM, Georg Otto wrote:
>
>> Hi,
>>
>> I tried to compile EMBOSS on a new computer running Mac OSX
>> 10.3 unfortunately, the compile process aborts with the
>> error message:
>>
>> /bin/sh ../libtool --mode=link gcc  -O2   -o aaindexextract
>>  aaindexextract.o ../nucleus/libnucleus.la
>> ../ajax/libajaxg.la ../ajax/libajax.la
>> ../plplot/libplplot.la -lX11  -lm
>> gcc -O2 -o .libs/aaindexextract aaindexextract.o
>>  ../nucleus/.libs/libnucleus.dylib
>> ../ajax/.libs/libajaxg.dylib ../ajax/.libs/libajax.dylib
>> ../plplot/.libs/libplplot.dylib -lX11 -lm
>> ld: can't locate file for: -lX11
>> make[2]: *** [aaindexextract] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>> As I understand, EMBOSS has problems with Mac?s X11. Is
>> there any way to get around this.
>>
>> Any help will be highly appreciated.
>>
>> Cheers,
>>
>> Georg
>>
>> -- 
>> Georg Wilhelm Otto
>> Max-Planck-Institute for Developmental Biology
>> Department 3 - Genetics
>> Spemannstrasse 35
>> D-72076 Tuebingen (Germany)
>> phone:   +49-7071-601393
>> e-mail: georg.otto at tuebingen.mpg.de
>>
>



From aengus.stewart at cancer.org.uk  Wed Dec 24 12:01:21 2003
From: aengus.stewart at cancer.org.uk (Aengus Stewart)
Date: Wed, 24 Dec 2003 12:01:21 +0000
Subject: [EMBOSS] Jemboss updating
In-Reply-To: <20031204185828.GA11119@bigben.ulb.ac.be>
References: <3FCDF797.8020309@md.huji.ac.il> <20031204185828.GA11119@bigben.ulb.ac.be>
Message-ID: <3FE98011.5080701@cancer.org.uk>

Hi, 

Would it be possible to clarify for me what is required to update JEMBOSS?

I am just getting round to updating EMBOSS/Jemboss.

Are there any parts of the installation process that need to be rerun from my previous full install for client-server access with EMBOSS 2.7.1/ Jemboss 1.1?

Or would just building EMBOSS 2.8 and placing the JARS for Jemboss 1.2.1 in the correct place be enough?


Regards
Aengus


-- 
----------------------------------------------------------------------------
Aengus Stewart
Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
----------------------------------------------------------------------------



From tcarver at rfcgr.mrc.ac.uk  Sat Dec 27 12:56:31 2003
From: tcarver at rfcgr.mrc.ac.uk (Dr T. Carver)
Date: Sat, 27 Dec 2003 12:56:31 +0000 (GMT)
Subject: [EMBOSS] Jemboss updating
In-Reply-To: <3FE98011.5080701@cancer.org.uk>
Message-ID: <Pine.SOL.4.44.0312271254160.13200-100000@bromine>


Hi Aengus

The easiest way to do this is to start from scratch, i.e. stop the
tomcat server and remove the old copy and allow the installation script
to install emboss/jemboss etc.

Cheers
Tim

Tim Carver
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: tcarver at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk


On Wed, 24 Dec 2003, Aengus Stewart wrote:

> Hi,
>
> Would it be possible to clarify for me what is required to update JEMBOSS?
>
> I am just getting round to updating EMBOSS/Jemboss.
>
> Are there any parts of the installation process that need to be rerun
> from my previous full install for client-server access with EMBOSS
> 2.7.1/ Jemboss 1.1?
>
>  Or would just building EMBOSS 2.8 and placing the JARS for Jemboss
> 1.2.1 in the correct place be enough?
>
>
> Regards
> Aengus
>
>
> --
> ----------------------------------------------------------------------------
> Aengus Stewart
> Computational Genome Analysis Laboratory  Tel: +44 (0)20 7269 3679
> Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
> ----------------------------------------------------------------------------
>



From ranrub at md.huji.ac.il  Sun Dec 28 16:03:44 2003
From: ranrub at md.huji.ac.il (Ran Rubinstein)
Date: Sun, 28 Dec 2003 18:03:44 +0200
Subject: [EMBOSS] Updating Emboss w/ SRS as gui
Message-ID: <000101c3cd5c$2b4d2ff0$7ea74084@sauron>

We are running EMBOSS 2.7.1 and SRS 7.1.1 (academic) as both the database
and a web front end. Does anyone have experience with newer emboss 2.8 and
SRS? Are the icarus (.i) files provided with SRS for using EMBOSS compatible
with the new version?

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



From kvddrift at earthlink.net  Mon Dec 29 17:30:41 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Mon, 29 Dec 2003 12:30:41 -0500
Subject: [EMBOSS] plplot question
Message-ID: <B98C5493-3A24-11D8-9AF6-003065A5FDCC@earthlink.net>

Hi,

Will it be a problem if I install emboss when an existing plplot 
package is already installed? If yes, is there a way to disable the 
plplot that comes with emboss from being installed so that emboss will 
use the already installed plplot?



thanks,

- Koen.