From charles-listes-emboss at plessy.org  Sun Aug  3 01:19:32 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 3 Aug 2008 14:19:32 +0900
Subject: [EMBOSS] Debian packages available for EMBOSS 6.0.1,
	in the `experimental' section.
In-Reply-To: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
Message-ID: <20080803051932.GA17654@kunpuu.plessy.org>

Le Wed, Jul 16, 2008 at 08:29:21PM +0100, ajb at ebi.ac.uk a ?crit :
> 
> EMBOSS 6.0.1 is now available from:
> 
>   ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz

Dear all,

Debian packages for EMBOSS 6.0.1 are currently available in the
`experimental' section of Debian:

http://packages.debian.org/experimental/emboss

A novelty with this update is the introduction of a new package,
`emboss-test', that contains the test directory of EMBOSS. During the
building of the `emboss' binary packages, the tests are ran and the
results can be seen in the build logs, for instance with the i386
architecture:

http://experimental.debian.net/fetch.php?&pkg=emboss&ver=6.0.1-1&arch=i386&stamp=1217462842&file=log&as=raw

We are currently in last steps for the preparation of the next Debian
stable release ("Lenny"), and it will be shipped with EMBOSS 5.0.0 with
all the latest patches plus the correction for using with clustalw2
that was posted on this list. After the Debian stable release, the 6.0.1
packages will be available in the usual `unstable' and `testing'
distributions.

The Debian binary packages for EMBASSY were built against version 5.0.0
of AJAX and NUCLEUS. Is it necessary to rebuild them against version
6.0.1?

have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

From d.gatherer at mrcvu.gla.ac.uk  Mon Aug  4 08:25:58 2008
From: d.gatherer at mrcvu.gla.ac.uk (Derek Gatherer)
Date: Mon, 04 Aug 2008 13:25:58 +0100
Subject: [EMBOSS] how string is shuffleseq
In-Reply-To: <20080803051932.GA17654@kunpuu.plessy.org>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
	<20080803051932.GA17654@kunpuu.plessy.org>
Message-ID: <E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>

Dear EMBOSS experts

How good a shuffler is shuffleseq?  I have always believed that it 
shuffles beyond all recognition, since tracer words inserted into a 
database are always gone after 1 round of shuffling.  But are there 
any hard test data on its shuffling strength?  For instance, for any, 
say, 100-mer, what fragments would reasonably be expected to remain 
after shuffling?  Should I be surprised to see a 15-mer from the 
100-mer still intact??

Sorry I can't express this more precisely.  I thinks it's probably 
clear...  I ask as there is a piece of software I am testing on real 
genomes and their shuffled derivatives, and I want to exclude the 
possibility that the control is compromised by an inadequacy of shuffling.

Cheers
Derek


From Jorrit.Boekel at ki.se  Mon Aug  4 10:34:43 2008
From: Jorrit.Boekel at ki.se (Jorrit Boekel)
Date: Mon, 4 Aug 2008 16:34:43 +0200
Subject: [EMBOSS] jaspscan - multiple sequences
Message-ID: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>

Dear all,

I have only today found and installed EMBOSS on an OSX10.4 computer,  
because I wanted to use jaspscan to feed multiple sequences to the  
JASPAR database at once. The tool seems to work alright, except when  
I try to enter multiple fasta sequences in one go. It analyzes/writes  
only the first seq and then exits with:

    EMBOSS An error in jaspscan.c at line 763:
Cannot open matrix file <null>

I could maybe write a script that feeds sequences one after one, but  
I'd like to do it the cleaner way.

Now, since I am very new to EMBOSS, I might be doing something very  
obvious wrong. Basically I do:
$ jaspscan
Scans DNA sequences for transcription factors
Input nucleotide sequence(s): test?.seq
Jaspar matrix set
          C : Core
          F : Fam
          P : Phylofacts
          N : CNE
          O : POLII
          S : SPLICE
Matrix set [C]:
Comma separated matrix list [all]:
Threshold percentage [80.0]:
Output report [fasta_test.jaspscan]:

And I have two files called test1.seq and test2.seq, which are both  
fasta formatted files. Each one can be analyzed in a single-file  
session, but there seems to be an error when processing the two of  
them. If anyone has an idea how to get this working I'd love to hear it.

Cheers,
jorrit


-- 
Jorrit Boekel

Ph.D. student
Dept. of Neuroscience
Karolinska Institutet





From db60 at st-andrews.ac.uk  Mon Aug  4 11:06:11 2008
From: db60 at st-andrews.ac.uk (Daniel Barker)
Date: Mon, 04 Aug 2008 16:06:11 +0100
Subject: [EMBOSS] how string is shuffleseq
In-Reply-To: <E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>	<20080803051932.GA17654@kunpuu.plessy.org>
	<E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>
Message-ID: <48971AE3.40806@st-andrews.ac.uk>

Dear Derek,

Not a direct answer to your question - but there was an interesting 
paper on shuffling recently, did you see it:

Jiang et al. (2008) uShuffle: A useful tool for shuffling biological 
sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.

Best wishes,

Daniel

Derek Gatherer wrote:
> Dear EMBOSS experts
> 
> How good a shuffler is shuffleseq?  I have always believed that it 
> shuffles beyond all recognition, since tracer words inserted into a 
> database are always gone after 1 round of shuffling.  But are there any 
> hard test data on its shuffling strength?  For instance, for any, say, 
> 100-mer, what fragments would reasonably be expected to remain after 
> shuffling?  Should I be surprised to see a 15-mer from the 100-mer still 
> intact??
> 
> Sorry I can't express this more precisely.  I thinks it's probably 
> clear...  I ask as there is a piece of software I am testing on real 
> genomes and their shuffled derivatives, and I want to exclude the 
> possibility that the control is compromised by an inadequacy of shuffling.
> 
> Cheers
> Derek
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

-- 
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

From ajb at ebi.ac.uk  Mon Aug  4 11:50:32 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 4 Aug 2008 16:50:32 +0100 (BST)
Subject: [EMBOSS] jaspscan - multiple sequences
In-Reply-To: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
References: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
Message-ID: <56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>

Dear Jorrit,

It was an oversight. The attached patch file should fix the
source code - it was created a while ago to help someone who
asked the same question. Go into the EMBOSS-6.0.1 directory and type:

gunzip -c /somewhere/jaspscan-patch.gz | patch -p1


then recompile. I am away at the moment but one of my colleagues will be
able to answer any further questions on this. The attached will become
part of an official patch sometime after I get back.

Alan


> Dear all,
>
> I have only today found and installed EMBOSS on an OSX10.4 computer,
> because I wanted to use jaspscan to feed multiple sequences to the
> JASPAR database at once. The tool seems to work alright, except when
> I try to enter multiple fasta sequences in one go. It analyzes/writes
> only the first seq and then exits with:
>
>     EMBOSS An error in jaspscan.c at line 763:
> Cannot open matrix file <null>
>
> I could maybe write a script that feeds sequences one after one, but
> I'd like to do it the cleaner way.
>
> Now, since I am very new to EMBOSS, I might be doing something very
> obvious wrong. Basically I do:
> $ jaspscan
> Scans DNA sequences for transcription factors
> Input nucleotide sequence(s): test?.seq
> Jaspar matrix set
>           C : Core
>           F : Fam
>           P : Phylofacts
>           N : CNE
>           O : POLII
>           S : SPLICE
> Matrix set [C]:
> Comma separated matrix list [all]:
> Threshold percentage [80.0]:
> Output report [fasta_test.jaspscan]:
>
> And I have two files called test1.seq and test2.seq, which are both
> fasta formatted files. Each one can be analyzed in a single-file
> session, but there seems to be an error when processing the two of
> them. If anyone has an idea how to get this working I'd love to hear it.
>
> Cheers,
> jorrit
>
>
> --
> Jorrit Boekel
>
> Ph.D. student
> Dept. of Neuroscience
> Karolinska Institutet
>
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
-------------- next part --------------
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From mathog at caltech.edu  Mon Aug  4 13:39:36 2008
From: mathog at caltech.edu (David Mathog)
Date: Mon, 04 Aug 2008 10:39:36 -0700
Subject: [EMBOSS] how string is shuffleseq
Message-ID: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>

> Not a direct answer to your question - but there was an interesting 
> paper on shuffling recently, did you see it:
> 
> Jiang et al. (2008) uShuffle: A useful tool for shuffling biological 
> sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.

An even less direct answer - I finally got around to rewriting and
generalizing my make_random_dna program from GCG/Fortran to
make_random_seq in standard C, with a GPL 2 license.  So now I can
finally distribute it, instead of having to tell people who ask for it
they can't have it because of licensing issues. 

This program does not maintain the tuple ratios exactly as would (some)
shuffle programs, but it comes arbitrarily close to doing so on a long
enough generated sequence.   It is normally used to generate control
sequences for other programs, as are the various shuffle programs.  The
original would only do DNA, the new one will do DNA, protein, ASCII, or
any specified subset of ASCII.  

It is available here:

http://saf.bio.caltech.edu/pub/software/molbio/make_random_seq.c

Regards,

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

From Jorrit.Boekel at ki.se  Tue Aug  5 05:01:48 2008
From: Jorrit.Boekel at ki.se (Jorrit Boekel)
Date: Tue, 5 Aug 2008 11:01:48 +0200
Subject: [EMBOSS] jaspscan - multiple sequences
In-Reply-To: <56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>
References: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
	<56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>
Message-ID: <7D30B26E-1E99-4C53-97D9-B8FC64C5964A@ki.se>

Hi,

Thanks for the patch! Works like a charm.

jorrit

On Aug 4, 2008, at 5:50 PM, ajb at ebi.ac.uk wrote:

> Dear Jorrit,
>
> It was an oversight. The attached patch file should fix the
> source code - it was created a while ago to help someone who
> asked the same question. Go into the EMBOSS-6.0.1 directory and type:
>
> gunzip -c /somewhere/jaspscan-patch.gz | patch -p1
>
>
> then recompile. I am away at the moment but one of my colleagues  
> will be
> able to answer any further questions on this. The attached will become
> part of an official patch sometime after I get back.
>
> Alan
>
>
>> Dear all,
>>
>> I have only today found and installed EMBOSS on an OSX10.4 computer,
>> because I wanted to use jaspscan to feed multiple sequences to the
>> JASPAR database at once. The tool seems to work alright, except when
>> I try to enter multiple fasta sequences in one go. It analyzes/writes
>> only the first seq and then exits with:
>>
>>     EMBOSS An error in jaspscan.c at line 763:
>> Cannot open matrix file <null>
>>
>> I could maybe write a script that feeds sequences one after one, but
>> I'd like to do it the cleaner way.
>>
>> Now, since I am very new to EMBOSS, I might be doing something very
>> obvious wrong. Basically I do:
>> $ jaspscan
>> Scans DNA sequences for transcription factors
>> Input nucleotide sequence(s): test?.seq
>> Jaspar matrix set
>>           C : Core
>>           F : Fam
>>           P : Phylofacts
>>           N : CNE
>>           O : POLII
>>           S : SPLICE
>> Matrix set [C]:
>> Comma separated matrix list [all]:
>> Threshold percentage [80.0]:
>> Output report [fasta_test.jaspscan]:
>>
>> And I have two files called test1.seq and test2.seq, which are both
>> fasta formatted files. Each one can be analyzed in a single-file
>> session, but there seems to be an error when processing the two of
>> them. If anyone has an idea how to get this working I'd love to  
>> hear it.
>>
>> Cheers,
>> jorrit
>>
>>
>> --
>> Jorrit Boekel
>>
>> Ph.D. student
>> Dept. of Neuroscience
>> Karolinska Institutet
>>
>>
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>> <jaspscan-patch.gz>


From peter.robinson at t-online.de  Tue Aug  5 05:50:51 2008
From: peter.robinson at t-online.de (Peter Robinson)
Date: Tue, 05 Aug 2008 11:50:51 +0200
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
 cannot open shared object file: No such file or directory
Message-ID: <4898227B.2000000@t-online.de>

Hi all,

I have tried to install EMBOSS 6.0 and got through ./configure, make, 
make install without error messages. However, when I try to start an 
emboss program, I get the following error:

error while loading shared libraries: libnucleus.so.6: cannot open 
shared object file: No such file or directory


I am running debian 4.0 & couldnt find any reference to this in google 
or the online docs. Any hints greatly appreciated!
-Peter


From charles-listes-emboss at plessy.org  Tue Aug  5 06:24:18 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Tue, 5 Aug 2008 19:24:18 +0900
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
	cannot open shared object file: No such file or directory
In-Reply-To: <4898227B.2000000@t-online.de>
References: <4898227B.2000000@t-online.de>
Message-ID: <20080805102418.GC12378@kunpuu.plessy.org>

Le Tue, Aug 05, 2008 at 11:50:51AM +0200, Peter Robinson a ?crit :
> 
> I have tried to install EMBOSS 6.0 and got through ./configure, make, 
> make install without error messages. However, when I try to start an 
> emboss program, I get the following error:
> 
> error while loading shared libraries: libnucleus.so.6: cannot open 
> shared object file: No such file or directory
> 
> I am running debian 4.0 & couldnt find any reference to this in google 
> or the online docs. Any hints greatly appreciated!

Hello Peter,

There are now Debian EMBOSS packages version 6.0.1 that can solve your
problem:

http://packages.debian.org/source/experimental/emboss

(The Jaspar patch sent earlier on this list is not yet applied, but will
be soon after it is posted on the EMBOSS FTP site).

Otherwise, you may collect a few more informations to better understand
your problem, with the following commands:

 - which seqret
 - ldd $(which seqret) | grep nucleus
 - ls -l $(ldd $(which seqret) | grep nucleus | cut -f3 -d' ')

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan

From shrish at ccmb.res.in  Tue Aug  5 05:54:32 2008
From: shrish at ccmb.res.in (Shrish Tiwari)
Date: Tue, 5 Aug 2008 15:24:32 +0530 (IST)
Subject: [EMBOSS] Fw:  requests for backtranseq
Message-ID: <143321688.1217930072219.JavaMail.root@127.0.0.1>

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Name: not available
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20080805/25fec8a2/attachment.pl>

From peter.robinson at t-online.de  Wed Aug  6 03:39:39 2008
From: peter.robinson at t-online.de (Peter Robinson)
Date: Wed, 06 Aug 2008 09:39:39 +0200
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
 cannot open shared object file: No such file or directory
In-Reply-To: <20080805102418.GC12378@kunpuu.plessy.org>
References: <4898227B.2000000@t-online.de>
	<20080805102418.GC12378@kunpuu.plessy.org>
Message-ID: <4899553B.1070704@t-online.de>

Charles Plessy wrote:
> Le Tue, Aug 05, 2008 at 11:50:51AM +0200, Peter Robinson a ?crit :
>   
>> I have tried to install EMBOSS 6.0 and got through ./configure, make, 
>> make install without error messages. However, when I try to start an 
>> emboss program, I get the following error:
>>
>> error while loading shared libraries: libnucleus.so.6: cannot open 
>> shared object file: No such file or directory
>>
>> I am running debian 4.0 & couldnt find any reference to this in google 
>> or the online docs. Any hints greatly appreciated!
>>     
>
>   





> Hello Peter,
>
> There are now Debian EMBOSS packages version 6.0.1 that can solve your
> problem:
>
> http://packages.debian.org/source/experimental/emboss
>
> (The Jaspar patch sent earlier on this list is not yet applied, but will
> be soon after it is posted on the EMBOSS FTP site).
>
> Otherwise, you may collect a few more informations to better understand
> your problem, with the following commands:
>
>  - which seqret
>  - ldd $(which seqret) | grep nucleus
>  - ls -l $(ldd $(which seqret) | grep nucleus | cut -f3 -d' ')
>
> Have a nice day,
>
>   
Hi Charles,

I want to use the emboss-ized PHYLIP programs, which do not seem to be 
in the debian package (the 5.0 package that is in testing).  I figured 
out what the problem is and am posting it here in case anybody else runs 
across the same problem.

1) The output of ldd $(which seqret) was:

peter at peter:~$ which seqret
/usr/local/bin/seqret
peter at peter:~$ seqret
seqret: error while loading shared libraries: libnucleus.so.6: cannot 
open shared object file: No such file or directory
peter at peter:~$ ldd $(which seqret)
        linux-gate.so.1 =>  (0xb7efc000)
        libnucleus.so.6 => not found
        libajaxg.so.6 => not found
        libajax.so.6 => not found
        libeplplot.so.3 => not found
        libX11.so.6 => /usr/lib/libX11.so.6 (0xb7deb000)
        libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7dc5000)
        libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7c6a000)
        libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb7c67000)
        libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7c4f000)
        libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb7c4b000)
        /lib/ld-linux.so.2 (0xb7efd000)
        libXau.so.6 => /usr/lib/libXau.so.6 (0xb7c48000)
        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7c43000)

2) I therefore was missing the shared library for plplot, which had 
apparently prevented the nucleus and ajax libraries from being properly 
installed. I installed the libplplot-dev debian package and went through 
configure-make-make install for EMBOSS-6.0.1 and PHYLIP and now 
everything works.

-thanks, Peter



From d.gatherer at mrcvu.gla.ac.uk  Thu Aug  7 10:50:55 2008
From: d.gatherer at mrcvu.gla.ac.uk (Derek Gatherer)
Date: Thu, 07 Aug 2008 15:50:55 +0100
Subject: [EMBOSS] how strong is shuffleseq (Summary)
In-Reply-To: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>
References: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>
Message-ID: <E1KR6pU-0001E3-00@hillhead.cent.gla.ac.uk>

Thanks to those who replied.

I compared shuffleseq with make_randon_dna (the latter with flags: -n 
-order 1).

The test was a piece of software that recognises certain complex 
patterns within genomes.  As controls for that pattern recognition 
process, the genomes were iteratively shuffled 100 times with both 
the shuffling applications (by iteratively I mean shuffle once then 
pipe the output back in to re-shuffle and so on).

There seemed to be no difference in the background scores for 
shuffling once, 10 times etc up to 100 times.  I therefore infer that 
the slight background rate that was troubling me is not an artefact 
of poor shuffing.

Therefore, the answer to the original question, I reckon, is: 
shuffleseq is just as good if you choose to shuffle once as to 
shuffle 100 times.  The same is true for make_randon_dna.  There is 
nothing to separate the two programs in performance.

D.


From mathog at caltech.edu  Thu Aug  7 15:29:35 2008
From: mathog at caltech.edu (David Mathog)
Date: Thu, 07 Aug 2008 12:29:35 -0700
Subject: [EMBOSS] how strong is shuffleseq (Summary)
Message-ID: <E1KRBB1-0006bq-Cf@mendel.bio.caltech.edu>

Derek Gatherer wrote:
> Therefore, the answer to the original question, I reckon, is: 
> shuffleseq is just as good if you choose to shuffle once as to 
> shuffle 100 times. The same is true for make_randon_dna.  

Actually, running make_random_seq twice in a row to generate a single
sequence is actually counterproductive.  If you do that the first run
will have a transition table which exactly matches those in the input
sequence, while the second run will generate a transition table from the
first randomized sequence, and since that is of finite length, the
second run will only obtain an approximation of the originally observed
transition frequencies for use in generating the final randomized
sequence.  The shorter the sequence, the greater this effect will be. 

>  There is 
> nothing to separate the two programs in performance.

The two randomized sequences should have slightly different properties. 

The output of shuffleseq will maintain composition (exactly), while the
output of make_random_seq, with the parameters you used, will maintain
dimer composition (approximately).  How different the random sequences
produced  by the two programs are will depend to a great extent on how
skewed the dimer composition of the input sequence was with respect to
the expected dimer composition (as calculated from the monomer
composition).  That is, if A,G,C,T are all 25%, and all dimers are
6.25%, the outputs of the two programs would be very similar.  However,
consider an extreme case which illustrates how much they can differ:

% echo AGCTAGCTAGCTAGCT \
  | make_random_seq -in - -inproc 2 -order 1 -n
>random_sequence_0
TAGCTAGCTAGCTAGC

Which is just the original sequence (phase shifted).  Similarly, for
this very short sequence, even -order 0 would be distinguishable:

% echo AGCTAGCTAGCTAGCT | make_random_seq -in - -inproc 2 -order 0 -n  
>random_sequence_0
GAAAGACTCTGTATGG

In this case resulting in a sequence with 5 G, 5 A, 4 T, 2 C, whereas
shuffleseq would still have exactly 4 of each.

Regards,

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

From john.walshaw at bbsrc.ac.uk  Mon Aug 18 13:37:50 2008
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Mon, 18 Aug 2008 18:37:50 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
Message-ID: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>

Hello,
 
I'm having trouble getting seqret to return the expected FASTA-header
style when using the 'ncbi' output sequence format, when applying it to
either the native UniProt data files or an EMBOSS database made from
them.
 
In the manual for seqret, in the section "Output Format...", this is the
description of the "ncbi" style of FASTA format:
 
ncbi multiple NCBI style FASTA format with the database name, entry
   name and accession number separated by pipe ("|") characters.

 
When I apply seqret to the current native-format UniProt files (Jul
22nd,UniProt release 14.0) with these arguments I get the following
FASTA-format headers:
 
seqret uniprot_sprot.dat -outseq stdout -osf ncbi | grep '^>' | head -5

 
>gnl|unk|104K_THEAN (Q4U9M9) RecName: Full=104 kDa microneme/rhoptry
antigen; AltName: Full=p104; Flags: Precursor;
>gnl|unk|104K_THEPA (P15711) RecName: Full=104 kDa microneme/rhoptry
antigen; AltName: Full=p104; Flags: Precursor;
>gnl|unk|108_SOLLC (Q43495) RecName: Full=Protein 108; Flags: Precursor;
>gnl|unk|10KD_VIGUN (P18646) RecName: Full=10 kDa protein; AltName:
Full=Clone PSAS10; Flags: Precursor;
>gnl|unk|110KD_PLAKN (P13813) RecName: Full=110 kDa antigen; AltName:
Full=PK110; Flags: Fragment;

- shouldn't this be something like this instead:
 
>unk|104K_THEAN|Q4U9M9  .....
>unk|104K_THEPA|P15711 ....
 
etc?
 
seqret seems to be identifying the ID and AccNo separately ok, because
if I specify 'fasta' or 'pearson' as the output format I get the
expected headers, i.e.:
 
>104K_THEAN Q4U9M9 RecName: Full=104 kDa microneme/rhoptry antigen;
AltName: Full=p104; Flags: Precursor;
 
etc.
 
I've found this behaviour in EMBOSS 5.0.0 and 6.0.1. If I apply seqret
to an EMBOSS database I've made by running dbxflat on the native UniProt
files, then -osf ncbi gives me the same format as when applied directly
to the files, except that the database name appears instead of 'unk'.
 
By the way, is there a way of making seqret return the same style header
as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
>db|id|accno), or is this what the ncbi format is intended to do?
 
best wishes,
 
Dr John Walshaw
Department of Computational & Systems Biology
John Innes Centre
Colney
Norwich NR4 7UH
UK
 
 


From emno72 at gmail.com  Mon Aug 18 23:06:46 2008
From: emno72 at gmail.com (Mohd Noor Mat Isa)
Date: Tue, 19 Aug 2008 11:06:46 +0800
Subject: [EMBOSS] EMBOSS 6 on SuSe SLES 10 ia64
Message-ID: <2e2159f50808182006u56b9f101v1042af4d820871be@mail.gmail.com>

Hi all,
I try to compile the EMBOSS 6 on my Itanium 2 server (SGI Altix4700) running
SuSe SLES 10. No errors are found during the compilation process... but I
can't run it. The error message as below:

"error while loading shared libraries: libnucleus.so.6: cannot open shared
object file: No such file or directory"

this is the report once I run ldd:

Altix4700:/home/emno # ldd $(which seqret)
        linux-gate.so.1 =>  (0xa000000000000000)
        libnucleus.so.6 => not found
        libajaxg.so.6 => not found
        libajax.so.6 => not found
        libeplplot.so.3 => not found
        libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x2000000000064000)
        libm.so.6.1 => /lib/libm.so.6.1 (0x2000000000238000)
        libc.so.6.1 => /lib/libc.so.6.1 (0x2000000000308000)
        libdl.so.2 => /lib/libdl.so.2 (0x2000000000558000)
        /lib/ld-linux-ia64.so.2 (0x2000000000000000)
Altix4700:/home/emno #

I try to find plplot rpm for suse ia64 to get this library but could not
find it .. anybody can help or give any sugestions

Thanks
Mohd Noor

From pmr at ebi.ac.uk  Tue Aug 19 04:29:46 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 19 Aug 2008 09:29:46 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
Message-ID: <48AA847A.2070808@ebi.ac.uk>

john walshaw (JIC) wrote:
  > I'm having trouble getting seqret to return the expected FASTA-header
> style when using the 'ncbi' output sequence format, when applying it to
> either the native UniProt data files or an EMBOSS database made from
> them.
>  
> In the manual for seqret, in the section "Output Format...", this is the
> description of the "ncbi" style of FASTA format:
>  
> ncbi multiple NCBI style FASTA format with the database name, entry
>    name and accession number separated by pipe ("|") characters.

This could be extended to explain that NCBI also have an annoyingly 
short list of valid database names. Any other name has to appear as 
"gnl|dbname", as you see for your uniprox database indexd with dbxflat. 
We use "unk" if we have no known database name, but we treat it as a 
general name - NCBI's "unk|identifier" is something special to them.

If you use one of the "NCBI list" database names, for example adding 
"-sdbname sp" to the command line, you will get a swissprot NCBI sandard 
identifier - but this is because "sp" is one of their special names. You 
cannot even assume the data is protein if you see "sp" in the identifier 
(genpept for example uses emb and gb as database names for protein 
sequences).

> By the way, is there a way of making seqret return the same style header
> as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
>> db|id|accno), or is this what the ncbi format is intended to do?

Hmmmm .... yet another FASTA format (and see below for another one). 
Yes, that looks like a good idea. We need an output name for it, perhaps 
wublast is the best choice.

You emntioned UniProt 14 - the latest release also includes extensions 
to the Fasta format description to tag species and other information. We 
are considering making this the default version of the FASTA format for 
EMBOSS so we can preserve more information - does this sound like a good 
idea?

For example: >sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry antigen 
OS=Theileria annulata GN=TA08425 PE=3 SV=1


Also on the subject of UniProt 14 - the .dat flat files have a new 
syntax for the DE lines. we had to ignore that as the cange appeared 
just before EMBOSS 6.0.0 Is anyone interested in having the details 
parsed out, or in having the original friendly description generated?

ID   104K_THEAN              Reviewed;         893 AA.
AC   Q4U9M9;
DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2005, sequence version 1.
DT   22-JUL-2008, entry version 18.
DE   RecName: Full=104 kDa microneme/rhoptry antigen;
DE   AltName: Full=p104;
DE   Flags: Precursor;

Hope this helps, even if it adds some new questions!

Peter

From john.walshaw at bbsrc.ac.uk  Tue Aug 19 05:25:36 2008
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Tue, 19 Aug 2008 10:25:36 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <48AA847A.2070808@ebi.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
	<48AA847A.2070808@ebi.ac.uk>
Message-ID: <E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>


Thanks for your help Peter, please see comments below. 

> -----Original Message-----
> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
> Sent: 19 August 2008 09:30
> To: john walshaw (JIC)
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] seqret output sequence format "ncbi"
> 
> john walshaw (JIC) wrote:
>   > I'm having trouble getting seqret to return the expected 
> FASTA-header
> > style when using the 'ncbi' output sequence format, when 
> applying it 
> > to either the native UniProt data files or an EMBOSS database made 
> > from them.
> >  
> > In the manual for seqret, in the section "Output 
> Format...", this is 
> > the description of the "ncbi" style of FASTA format:
> >  
> > ncbi multiple NCBI style FASTA format with the database name, entry
> >    name and accession number separated by pipe ("|") characters.
> 
> This could be extended to explain that NCBI also have an 
> annoyingly short list of valid database names. Any other name 
> has to appear as "gnl|dbname", as you see for your uniprox 
> database indexd with dbxflat. 
> We use "unk" if we have no known database name, but we treat 
> it as a general name - NCBI's "unk|identifier" is something 
> special to them.
> 
> If you use one of the "NCBI list" database names, for example 
> adding "-sdbname sp" to the command line, you will get a 
> swissprot NCBI sandard identifier - but this is because "sp" 
> is one of their special names. You cannot even assume the 
> data is protein if you see "sp" in the identifier (genpept 
> for example uses emb and gb as database names for protein sequences).
> 

Thanks, I see, that does it. So if I had named my database 'sp' instead
of 'uniprot' this would have worked automatically. 

> > By the way, is there a way of making seqret return the same style 
> > header as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
> >> db|id|accno), or is this what the ncbi format is intended to do?
> 
> Hmmmm .... yet another FASTA format (and see below for another one). 
> Yes, that looks like a good idea. We need an output name for 
> it, perhaps wublast is the best choice.
> 

BTW the reason I ask this is that sp2fasta doesn't seem able to handle
the format changes in the DE line which have appeared in release 14.0.
My theory is that the format change, re below, occasionally makes
some DE lines very long, and too long for sp2fasta to read, so the
final continuation character (semicolon) is missed. This means that
if the next line is also a DE line, sp2fasta halts with a fatal error
about there being multiple definition lines for one sequence record.
Examples in release 14.0 are Q5IGR8 (in uniprot_sprot.dat) and A0B5I3
(in uniprot_trembl.dat). If there's a v. long DE line but the next
line isn't a DE line, then it doesn't matter and sp2fasta is ok.

> You emntioned UniProt 14 - the latest release also includes 
> extensions to the Fasta format description to tag species and 
> other information. We are considering making this the default 
> version of the FASTA format for EMBOSS so we can preserve 
> more information - does this sound like a good idea?
> 
> For example: >sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry 
> antigen OS=Theileria annulata GN=TA08425 PE=3 SV=1
> 

Personally, I think this would be a good idea. I'm assuming that
EMBOSS progs would themselves be able to parse these fields from the
FASTA headers?

> 
> Also on the subject of UniProt 14 - the .dat flat files have a new 
> syntax for the DE lines. we had to ignore that as the cange appeared 
> just before EMBOSS 6.0.0 Is anyone interested in having the details 
> parsed out, or in having the original friendly description generated?
> 
> ID   104K_THEAN              Reviewed;         893 AA.
> AC   Q4U9M9;
> DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
> DT   05-JUL-2005, sequence version 1.
> DT   22-JUL-2008, entry version 18.
> DE   RecName: Full=104 kDa microneme/rhoptry antigen;
> DE   AltName: Full=p104;
> DE   Flags: Precursor;

Having the option to parse them out would be useful :) These multiple
names can be a bit awkward sometimes, so if UniProt and EMBOSS do some
of the work for you, that's got to be good.

> 
> Hope this helps, even if it adds some new questions!
> 

Certainly does, many thanks again.

cheers

John

> Peter
> 


From pmr at ebi.ac.uk  Tue Aug 19 05:52:42 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 19 Aug 2008 10:52:42 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
	<48AA847A.2070808@ebi.ac.uk>
	<E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>
Message-ID: <48AA97EA.4090106@ebi.ac.uk>

john walshaw (JIC) wrote:
> Thanks for your help Peter, please see comments below. 
>> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
>> Sent: 19 August 2008 09:30
>> You emntioned UniProt 14 - the latest release also includes 
>> extensions to the Fasta format description to tag species and 
>> other information. We are considering making this the default 
>> version of the FASTA format for EMBOSS so we can preserve 
>> more information - does this sound like a good idea?
> 
> Personally, I think this would be a good idea. I'm assuming that
> EMBOSS progs would themselves be able to parse these fields from the
> FASTA headers?

Yes ... assuming they fit the expected format. We have to hope that no
other "FASTA" format is using something similar. UniProt has a very
limited set of XX= tags - depending on which part of UniProt you look at.

>> Also on the subject of UniProt 14 - the .dat flat files have a new 
>> syntax for the DE lines. we had to ignore that as the cange appeared 
>> just before EMBOSS 6.0.0 Is anyone interested in having the details 
>> parsed out, or in having the original friendly description generated?
> 
> Having the option to parse them out would be useful :) These multiple
> names can be a bit awkward sometimes, so if UniProt and EMBOSS do some
> of the work for you, that's got to be good.

Thanks. We will try to parse them. If we can generate the equivalent
UniProt 13 descriptions then we will know we have a reasonable parser.

If we can parse them ... my preference would be to use the old-style
descriptions. Only UniProt seems to be using this new split in their 
releases.

regards,

Peter


From dalloliogm at gmail.com  Wed Aug 20 04:17:26 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Wed, 20 Aug 2008 10:17:26 +0200
Subject: [EMBOSS] SeaView
In-Reply-To: <C4A53ED6.A492%staffa@niehs.nih.gov>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
Message-ID: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>

On Fri, Jul 18, 2008 at 12:24 AM, Staffa, Nick (NIH/NIEHS) <
staffa at niehs.nih.gov> wrote:

>
> I would really appreciate any evaluation of the editor SEAVIEW by anyone
> reading this. In reading the paper by Galtier,Gouy and Gautier,
>


Hi all,
I thought this discussion was so interesting, that I have opened a section
in wikipedia to discuss all sequence alignment editor software, starting
from those that you have described here.

Can you please have a look at this link:
-
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Alignment_Viewers.2FEditors
and tell me if it is ok, or if you have more suggestions.

I was thinking I could also put mega[1] as a sequence alignment editor
program. In fact, with this software you can edit alignments, even if the
program is made for making phylogenetics analysis.
What do you think?


[1] http://www.megasoftware.net/


>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Enterprise-Wide Information Technology Support Contract
> (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



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

My Blog on Bioinformatics (italian): http://bioinfoblog.it

From gbottu at vub.ac.be  Wed Aug 20 04:59:51 2008
From: gbottu at vub.ac.be (Guy Bottu)
Date: Wed, 20 Aug 2008 10:59:51 +0200
Subject: [EMBOSS] SeaView
In-Reply-To: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
	<5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
Message-ID: <48ABDD07.1000307@vub.ac.be>

Giovanni Marco Dall'Olio wrote:
> I thought this discussion was so interesting, that I have opened a section
> in wikipedia to discuss all sequence alignment editor software, starting
> from those that you have described here.

Nice initative !

A remark : the latest version of SeaView I have seen supports clustalw and 
muscle for re-alignment, not t-coffee (although you can re-configure SeaView to 
put any alignment software in).

Some other software that could be mentioned :
- Genedoc (very useful for preparing alignments for publication)
   http://www.nrbsc.org/gfx/genedoc

- SeqPup
   http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/

- MSE (text-mode, also embossified version available as Embassy package)

	Regards,
	Guy Bottu,
	BEN


From staffa at niehs.nih.gov  Wed Aug 20 10:11:13 2008
From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C])
Date: Wed, 20 Aug 2008 10:11:13 -0400
Subject: [EMBOSS] SeaView
In-Reply-To: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
	<5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
Message-ID: <7930EE6CD7CA354D93B444D0433C0611068488EB@NIHCESMLBX6.nih.gov>

It's nice to know, for once, who the author of a Wikipedia article is.

Nickolas G. Staffa, Jr. Ph.D.
Telephone: 919-316-4569  (NIEHS: 6-4569) 
Scientific Computing Support Group
NIEHS E-WITS Contract 
Science Task Monitor: Roy W. Reter ( reter at niehs.nih.gov )
National Institute of Environmental Health Sciences 
National Institutes of Health 
Research Triangle Park, North Carolina
 

-----Original Message-----
From: Giovanni Marco Dall'Olio [mailto:dalloliogm at gmail.com] 
Sent: Wednesday, August 20, 2008 4:17 AM
To: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] SeaView

On Fri, Jul 18, 2008 at 12:24 AM, Staffa, Nick (NIH/NIEHS) <
staffa at niehs.nih.gov> wrote:

>
> I would really appreciate any evaluation of the editor SEAVIEW by
anyone
> reading this. In reading the paper by Galtier,Gouy and Gautier,
>


Hi all,
I thought this discussion was so interesting, that I have opened a
section
in wikipedia to discuss all sequence alignment editor software, starting
from those that you have described here.

Can you please have a look at this link:
-
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Alignme
nt_Viewers.2FEditors
and tell me if it is ok, or if you have more suggestions.

I was thinking I could also put mega[1] as a sequence alignment editor
program. In fact, with this software you can edit alignments, even if
the
program is made for making phylogenetics analysis.
What do you think?


[1] http://www.megasoftware.net/


>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Enterprise-Wide Information Technology Support Contract
> (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



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

My Blog on Bioinformatics (italian): http://bioinfoblog.it
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss


From marcusclaesson at gmail.com  Tue Aug 26 06:07:04 2008
From: marcusclaesson at gmail.com (Marcus Claesson)
Date: Tue, 26 Aug 2008 12:07:04 +0200
Subject: [EMBOSS] can vectorstrip deal with indels?
Message-ID: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>

Hi,

According to the docs of vectorstrip it has a mismatch parameter which sets
the max allowed mismatch as a percentage. However, my input sequences
sometimes contain not just a mismatched character, but also a nucletide
insertion/deletion. It seems like vectorstrip can't handle this. Is this
correct or is there a way to introduce indels as well?

Many thanks,
Marcus

From ajb at ebi.ac.uk  Wed Aug 27 04:33:10 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 27 Aug 2008 09:33:10 +0100 (BST)
Subject: [EMBOSS] First 6.0.1 fixes available
Message-ID: <55051.86.9.126.186.1219825990.squirrel@webmail.ebi.ac.uk>

Some fixes are now available on the ftp server for EMBOSS 6.0.1 in
the usual places (for UNIX users):

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/

For most sites, using the 'patches' method will be the most
convenient (read the README in that directory).

The fixes are:

Fix 1. EMBOSS-6.0.1/emboss/jaspscan.c
       EMBOSS-6.0.1/nucleus/embprop.c

26 Aug 2008: jaspscan can now scan multiple sequences.
             "digest -allpartials" now reports all C-term fragments


For mEMBOSS (Windows) users the following setup file is a replacement
for the main release (6.0.1) and contains the above fixes. It
is constructed from the CVS code and so has 'beta' status. This file
also contains some fixes to the GUI. It also contains applications,
new to EMBOSS 6, which were in the UNIX version but didn't make it
into the mEMBOSS 6.0.1 release. You should uninstall any
current mEMBOSS installation before installing any new setup file.

ftp://emboss.open-bio.org/pub/EMBOSS/windows/beta/mEMBOSS-6.0.1.1-setup.exe


Alan



From pmr at ebi.ac.uk  Wed Aug 27 06:36:13 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 27 Aug 2008 11:36:13 +0100
Subject: [EMBOSS] can vectorstrip deal with indels?
In-Reply-To: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>
References: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>
Message-ID: <48B52E1D.9070808@ebi.ac.uk>

Marcus Claesson wrote:
> Hi,
> 
> According to the docs of vectorstrip it has a mismatch parameter which sets
> the max allowed mismatch as a percentage. However, my input sequences
> sometimes contain not just a mismatched character, but also a nucleotide
> insertion/deletion. It seems like vectorstrip can't handle this. Is this
> correct or is there a way to introduce indels as well?

Vectorstrip uses the EMBOSS pattern matching routines. These support
mismatches but not indels.

One possibility is to modify vectorstrip to define all possible indels
in the linker sequences. We can look into the performance impact.

Thanks for the sugestion

Peter Rice

From golharam at umdnj.edu  Sat Aug 23 14:33:17 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 23 Aug 2008 14:33:17 -0400
Subject: [EMBOSS] DOMAINATRIX compile error
Message-ID: <48B057ED.6000104@umdnj.edu>

So I''ve finally got around to building RPMs for EMBOSS 6.0.1 on RHEL5. 
  I got EMBOSS to build just fine and the RPMs look good.

Now, I'm working on building the EMBASSY packages.  I started with 
DOMAINATRIX and ran into a compiler error:

domainreso.c: In function ?main?:
domainreso.c:150: warning: ?ajFileNewIn? is deprecated (declared at 
/usr/include/ajfile.h:461)
domainseqs.c: In function ?main?:
domainseqs.c:176: warning: ?ajFileNewDirF? is deprecated (declared at 
/usr/include/ajfile.h:507)
domainseqs.c:180: warning: ?ajDirExt? is deprecated (declared at 
/usr/include/ajfile.h:453)
domainseqs.c: In function ?domainseqs_AlignDomain?:
domainseqs.c:485: warning: passing argument 12 of ?embAlignWalkNWMatrix? 
from incompatible pointer type
domainseqs.c:485: error: too many arguments to function 
?embAlignWalkNWMatrix?
make[2]: *** [domainseqs.o] Error 1


Any ideas?

Ryan

From golharam at umdnj.edu  Sat Aug 23 14:41:59 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 23 Aug 2008 14:41:59 -0400
Subject: [EMBOSS] DOMAINATRIX compile error
In-Reply-To: <48B057ED.6000104@umdnj.edu>
References: <48B057ED.6000104@umdnj.edu>
Message-ID: <48B059F7.1060302@umdnj.edu>

Ignore my message.  I didn't move the new tarball in place when 
rebuilding.

Ryan Golhar wrote:
> So I''ve finally got around to building RPMs for EMBOSS 6.0.1 on RHEL5. 
>  I got EMBOSS to build just fine and the RPMs look good.
> 
> Now, I'm working on building the EMBASSY packages.  I started with 
> DOMAINATRIX and ran into a compiler error:
> 
> domainreso.c: In function ?main?:
> domainreso.c:150: warning: ?ajFileNewIn? is deprecated (declared at 
> /usr/include/ajfile.h:461)
> domainseqs.c: In function ?main?:
> domainseqs.c:176: warning: ?ajFileNewDirF? is deprecated (declared at 
> /usr/include/ajfile.h:507)
> domainseqs.c:180: warning: ?ajDirExt? is deprecated (declared at 
> /usr/include/ajfile.h:453)
> domainseqs.c: In function ?domainseqs_AlignDomain?:
> domainseqs.c:485: warning: passing argument 12 of ?embAlignWalkNWMatrix? 
> from incompatible pointer type
> domainseqs.c:485: error: too many arguments to function 
> ?embAlignWalkNWMatrix?
> make[2]: *** [domainseqs.o] Error 1
> 
> 
> Any ideas?
> 
> Ryan
> 

From charles-listes-emboss at plessy.org  Wed Aug 27 10:05:20 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Wed, 27 Aug 2008 23:05:20 +0900
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
In-Reply-To: <48B059F7.1060302@umdnj.edu>
References: <48B057ED.6000104@umdnj.edu> <48B059F7.1060302@umdnj.edu>
Message-ID: <20080827140520.GC18561@kunpuu.plessy.org>

Le Sat, Aug 23, 2008 at 02:41:59PM -0400, Ryan Golhar a ?crit :
> Ignore my message.  I didn't move the new tarball in place when  
> rebuilding.

Ouch, the contents of the tarballs seem to have been updated while their
version number was left unchanged. We distribute domainatrix and
domalign in Debian, under the version 0.1.0, but older tarballs from the
EMBOSS 5.o release? Do you think that you can increment the version
number of the new ones on the EMBOSS FTP site? Otherwise we will make an
update under a version number like 0.1.0+20071507?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

From golharam at umdnj.edu  Wed Aug 27 10:33:45 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Wed, 27 Aug 2008 14:33:45 +0000
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
Message-ID: <287101333-1219847642-cardhu_decombobulator_blackberry.rim.net-1345440591-@bxe104.bisx.prod.on.blackberry>

I agree, the version numbers should be updated, however they never were in the past.  I update the release number of the RPMs to reflect the change.
------Original Message------
From: Charles Plessy
Sender: emboss-bounces at lists.open-bio.org
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
Sent: Aug 27, 2008 9:05 AM

Le Sat, Aug 23, 2008 at 02:41:59PM -0400, Ryan Golhar a ?crit :
> Ignore my message.  I didn't move the new tarball in place when  
> rebuilding.

Ouch, the contents of the tarballs seem to have been updated while their
version number was left unchanged. We distribute domainatrix and
domalign in Debian, under the version 0.1.0, but older tarballs from the
EMBOSS 5.o release? Do you think that you can increment the version
number of the new ones on the EMBOSS FTP site? Otherwise we will make an
update under a version number like 0.1.0+20071507?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss


Sent from my Verizon Wireless BlackBerry


From benys at usp.br  Thu Aug 28 19:25:37 2008
From: benys at usp.br (Beny Spira)
Date: Thu, 28 Aug 2008 20:25:37 -0300
Subject: [EMBOSS] jemboss
Message-ID: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>

Hi all
I've been trying to install jemboss as 'standalone' in my laptop. Its OS is
Linux Debian sid. I've previously installed jemboss in a PC running Mandriva
without any problems. But in Debian I get the following message:

------------------------- WARNING ----------------------------

The script has detected that /usr/include/gd.h
does not exist

Download gd from
       http://www.boutell.com/gd/

For details see the EMBOSS admin guide:
http://emboss.sourceforge.net/admin/

To exit use Control C or press return to continue.
-----------------------------------------------------------------------

gd.h is in /usr/include and libpng is also installed, so I don't know what
the problem is.

Any help would be appreciated,
Beny


-- 
Beny Spira
Departamento de Microbiologia
Instituto de Ci?ncias Biom?dicas
Universidade de S?o Paulo
Av. Prof. Lineu Prestes 1374
S?o Paulo-SP CEP:05508-900
Brasil
Tel: 5511-3091-7347
FAX: 5511-3091-7354
E-mail: benys at usp.br
Homepage: www.icb.usp.br/~benys


From ajb at ebi.ac.uk  Fri Aug 29 04:00:03 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 29 Aug 2008 09:00:03 +0100 (BST)
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
Message-ID: <55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>

Hi,

Looking at the script that message is indeed misleading. It will happen
if the script (in the case of Debian) can't find libgd.so.
I don't have a Debian installation to hand but I believe the
package you need to install is libgd2-dev (Debian users on this list will
correct me if I'm wrong). Installing that package should pull in all other
required dependencies for GD/PNG.

HTH

Alan

> Hi all
> I've been trying to install jemboss as 'standalone' in my laptop. Its OS
> is
> Linux Debian sid. I've previously installed jemboss in a PC running
> Mandriva
> without any problems. But in Debian I get the following message:
>
> ------------------------- WARNING ----------------------------
>
> The script has detected that /usr/include/gd.h
> does not exist
>
> Download gd from
>        http://www.boutell.com/gd/
>
> For details see the EMBOSS admin guide:
> http://emboss.sourceforge.net/admin/
>
> To exit use Control C or press return to continue.
> -----------------------------------------------------------------------
>
> gd.h is in /usr/include and libpng is also installed, so I don't know what
> the problem is.
>
> Any help would be appreciated,
> Beny
>
>
> --
> Beny Spira
> Departamento de Microbiologia
> Instituto de Ci?ncias Biom?dicas
> Universidade de S?o Paulo
> Av. Prof. Lineu Prestes 1374
> S?o Paulo-SP CEP:05508-900
> Brasil
> Tel: 5511-3091-7347
> FAX: 5511-3091-7354
> E-mail: benys at usp.br
> Homepage: www.icb.usp.br/~benys
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From charles-listes-emboss at plessy.org  Fri Aug 29 05:08:45 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 29 Aug 2008 18:08:45 +0900
Subject: [EMBOSS] jemboss
In-Reply-To: <55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
Message-ID: <20080829090845.GG15089@kunpuu.plessy.org>

Le Fri, Aug 29, 2008 at 09:00:03AM +0100, ajb at ebi.ac.uk a ?crit :
> 
> I don't have a Debian installation to hand but I believe the
> package you need to install is libgd2-dev (Debian users on this list will
> correct me if I'm wrong). Installing that package should pull in all other
> required dependencies for GD/PNG.

Hi,

a very useful tool for that kind of situations on Debian systems is
`apt-file':

anx159?~?$ apt-file search include/gd.h
libgd2-noxpm-dev: /usr/include/gd.h
libgd2-xpm-dev: /usr/include/gd.h

There is a very unforunate dichotomy of the GD library on Debian. I
would recommend to use libgd2-xpm-dev unless you really need to have XPM
support disabled.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan

From benys at usp.br  Fri Aug 29 11:21:43 2008
From: benys at usp.br (Beny Spira)
Date: Fri, 29 Aug 2008 12:21:43 -0300
Subject: [EMBOSS] jemboss
In-Reply-To: <20080829090845.GG15089@kunpuu.plessy.org>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
Message-ID: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>

Thanks for the answers. The libgd2-devel package was indeed missing. I
installed libgd2-xpm-dev and jemboss installation went smoothly.
However, I can't run jemboss, there is no response to the command
./runJemboss.sh
I checked the permissions and it is OK.
I even installed the entire EMBOSS package again, but still cannot make it
work.
Any clue what might be wrong?
Beny


On Fri, Aug 29, 2008 at 6:08 AM, Charles Plessy <
charles-listes-emboss at plessy.org> wrote:

> Le Fri, Aug 29, 2008 at 09:00:03AM +0100, ajb at ebi.ac.uk a ?crit :
> >
> > I don't have a Debian installation to hand but I believe the
> > package you need to install is libgd2-dev (Debian users on this list will
> > correct me if I'm wrong). Installing that package should pull in all
> other
> > required dependencies for GD/PNG.
>
> Hi,
>
> a very useful tool for that kind of situations on Debian systems is
> `apt-file':
>
> anx159?~?$ apt-file search include/gd.h
> libgd2-noxpm-dev: /usr/include/gd.h
> libgd2-xpm-dev: /usr/include/gd.h
>
> There is a very unforunate dichotomy of the GD library on Debian. I
> would recommend to use libgd2-xpm-dev unless you really need to have XPM
> support disabled.
>
> Have a nice day,
>
> --
> Charles Plessy
> Debian Med packaging team
> Tsurumi, Kanagawa, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



-- 
Beny Spira
Departamento de Microbiologia
Instituto de Ci?ncias Biom?dicas
Universidade de S?o Paulo
Av. Prof. Lineu Prestes 1374
S?o Paulo-SP CEP:05508-900
Brasil
Tel: 5511-3091-7347
FAX: 5511-3091-7354
E-mail: benys at usp.br
Homepage: www.icb.usp.br/~benys


From uludag at ebi.ac.uk  Fri Aug 29 14:43:03 2008
From: uludag at ebi.ac.uk (uludag at ebi.ac.uk)
Date: Fri, 29 Aug 2008 19:43:03 +0100 (BST)
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
	<21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
Message-ID: <59214.86.133.34.209.1220035383.squirrel@webmail.ebi.ac.uk>

Hi Beny,

You should have a line something similar to the following in your
runJemboss.sh

   /foo/java org.emboss.jemboss.Jemboss &

Can you try running "/foo/java -version" to check whether your java is
responding?

Is it supplied by Sun?

Jemboss install procedure doesn't automatically add the parameter "local"
to the java command line which is necessary when starting Jemboss in
standalone mode. If you haven't already done it modified command line
should look like

  /foo/java org.emboss.jemboss.Jemboss local &

Regards,
Mahmut

> I can't run jemboss, there is no response to the command
> ./runJemboss.sh
> I checked the permissions and it is OK.
> I even installed the entire EMBOSS package again, but still cannot make it
> work.
> Any clue what might be wrong?
>



From charles-listes-emboss at plessy.org  Fri Aug 29 21:50:14 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sat, 30 Aug 2008 10:50:14 +0900
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
	<21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
Message-ID: <20080830015014.GB19735@kunpuu.plessy.org>

Le Fri, Aug 29, 2008 at 12:21:43PM -0300, Beny Spira a ?crit :
> Thanks for the answers. The libgd2-devel package was indeed missing. I
> installed libgd2-xpm-dev and jemboss installation went smoothly.
> However, I can't run jemboss, there is no response to the command
> ./runJemboss.sh
> I checked the permissions and it is OK.
> I even installed the entire EMBOSS package again, but still cannot make it
> work.
> Any clue what might be wrong?

Maybe you forgot to give the path to the jdk when calling the configure
script?

If you use the non-free Sun Java package distributed by Debian (Lenny
release), the following option should do the job:

--with-java=/usr/lib/jvm/java-6-sun-1.6.0.07/include --with-javaos=/usr/lib/jvm/java-6-sun-1.6.0.07/include/linux

The freed version of Sun Java is unfortunately not ready yet, and I do
not know if jemboss works with alternatives (gcj, ...). If it were so,
please contact me, and I will make an official jemboss package for
Debian. If not, we will have to wait for "IcedTea" to be ready.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan

From charles-listes-emboss at plessy.org  Sun Aug  3 05:19:32 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sun, 3 Aug 2008 14:19:32 +0900
Subject: [EMBOSS] Debian packages available for EMBOSS 6.0.1,
	in the `experimental' section.
In-Reply-To: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
Message-ID: <20080803051932.GA17654@kunpuu.plessy.org>

Le Wed, Jul 16, 2008 at 08:29:21PM +0100, ajb at ebi.ac.uk a ?crit :
> 
> EMBOSS 6.0.1 is now available from:
> 
>   ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.0.1.tar.gz

Dear all,

Debian packages for EMBOSS 6.0.1 are currently available in the
`experimental' section of Debian:

http://packages.debian.org/experimental/emboss

A novelty with this update is the introduction of a new package,
`emboss-test', that contains the test directory of EMBOSS. During the
building of the `emboss' binary packages, the tests are ran and the
results can be seen in the build logs, for instance with the i386
architecture:

http://experimental.debian.net/fetch.php?&pkg=emboss&ver=6.0.1-1&arch=i386&stamp=1217462842&file=log&as=raw

We are currently in last steps for the preparation of the next Debian
stable release ("Lenny"), and it will be shipped with EMBOSS 5.0.0 with
all the latest patches plus the correction for using with clustalw2
that was posted on this list. After the Debian stable release, the 6.0.1
packages will be available in the usual `unstable' and `testing'
distributions.

The Debian binary packages for EMBASSY were built against version 5.0.0
of AJAX and NUCLEUS. Is it necessary to rebuild them against version
6.0.1?

have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


From d.gatherer at mrcvu.gla.ac.uk  Mon Aug  4 12:25:58 2008
From: d.gatherer at mrcvu.gla.ac.uk (Derek Gatherer)
Date: Mon, 04 Aug 2008 13:25:58 +0100
Subject: [EMBOSS] how string is shuffleseq
In-Reply-To: <20080803051932.GA17654@kunpuu.plessy.org>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>
	<20080803051932.GA17654@kunpuu.plessy.org>
Message-ID: <E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>

Dear EMBOSS experts

How good a shuffler is shuffleseq?  I have always believed that it 
shuffles beyond all recognition, since tracer words inserted into a 
database are always gone after 1 round of shuffling.  But are there 
any hard test data on its shuffling strength?  For instance, for any, 
say, 100-mer, what fragments would reasonably be expected to remain 
after shuffling?  Should I be surprised to see a 15-mer from the 
100-mer still intact??

Sorry I can't express this more precisely.  I thinks it's probably 
clear...  I ask as there is a piece of software I am testing on real 
genomes and their shuffled derivatives, and I want to exclude the 
possibility that the control is compromised by an inadequacy of shuffling.

Cheers
Derek



From Jorrit.Boekel at ki.se  Mon Aug  4 14:34:43 2008
From: Jorrit.Boekel at ki.se (Jorrit Boekel)
Date: Mon, 4 Aug 2008 16:34:43 +0200
Subject: [EMBOSS] jaspscan - multiple sequences
Message-ID: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>

Dear all,

I have only today found and installed EMBOSS on an OSX10.4 computer,  
because I wanted to use jaspscan to feed multiple sequences to the  
JASPAR database at once. The tool seems to work alright, except when  
I try to enter multiple fasta sequences in one go. It analyzes/writes  
only the first seq and then exits with:

    EMBOSS An error in jaspscan.c at line 763:
Cannot open matrix file <null>

I could maybe write a script that feeds sequences one after one, but  
I'd like to do it the cleaner way.

Now, since I am very new to EMBOSS, I might be doing something very  
obvious wrong. Basically I do:
$ jaspscan
Scans DNA sequences for transcription factors
Input nucleotide sequence(s): test?.seq
Jaspar matrix set
          C : Core
          F : Fam
          P : Phylofacts
          N : CNE
          O : POLII
          S : SPLICE
Matrix set [C]:
Comma separated matrix list [all]:
Threshold percentage [80.0]:
Output report [fasta_test.jaspscan]:

And I have two files called test1.seq and test2.seq, which are both  
fasta formatted files. Each one can be analyzed in a single-file  
session, but there seems to be an error when processing the two of  
them. If anyone has an idea how to get this working I'd love to hear it.

Cheers,
jorrit


-- 
Jorrit Boekel

Ph.D. student
Dept. of Neuroscience
Karolinska Institutet






From db60 at st-andrews.ac.uk  Mon Aug  4 15:06:11 2008
From: db60 at st-andrews.ac.uk (Daniel Barker)
Date: Mon, 04 Aug 2008 16:06:11 +0100
Subject: [EMBOSS] how string is shuffleseq
In-Reply-To: <E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>
References: <34749.81.98.242.91.1216236561.squirrel@webmail.ebi.ac.uk>	<20080803051932.GA17654@kunpuu.plessy.org>
	<E1KPz8V-00044D-00@hillend.cent.gla.ac.uk>
Message-ID: <48971AE3.40806@st-andrews.ac.uk>

Dear Derek,

Not a direct answer to your question - but there was an interesting 
paper on shuffling recently, did you see it:

Jiang et al. (2008) uShuffle: A useful tool for shuffling biological 
sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.

Best wishes,

Daniel

Derek Gatherer wrote:
> Dear EMBOSS experts
> 
> How good a shuffler is shuffleseq?  I have always believed that it 
> shuffles beyond all recognition, since tracer words inserted into a 
> database are always gone after 1 round of shuffling.  But are there any 
> hard test data on its shuffling strength?  For instance, for any, say, 
> 100-mer, what fragments would reasonably be expected to remain after 
> shuffling?  Should I be surprised to see a 15-mer from the 100-mer still 
> intact??
> 
> Sorry I can't express this more precisely.  I thinks it's probably 
> clear...  I ask as there is a piece of software I am testing on real 
> genomes and their shuffled derivatives, and I want to exclude the 
> possibility that the control is compromised by an inadequacy of shuffling.
> 
> Cheers
> Derek
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

-- 
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532


From ajb at ebi.ac.uk  Mon Aug  4 15:50:32 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Mon, 4 Aug 2008 16:50:32 +0100 (BST)
Subject: [EMBOSS] jaspscan - multiple sequences
In-Reply-To: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
References: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
Message-ID: <56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>

Dear Jorrit,

It was an oversight. The attached patch file should fix the
source code - it was created a while ago to help someone who
asked the same question. Go into the EMBOSS-6.0.1 directory and type:

gunzip -c /somewhere/jaspscan-patch.gz | patch -p1


then recompile. I am away at the moment but one of my colleagues will be
able to answer any further questions on this. The attached will become
part of an official patch sometime after I get back.

Alan


> Dear all,
>
> I have only today found and installed EMBOSS on an OSX10.4 computer,
> because I wanted to use jaspscan to feed multiple sequences to the
> JASPAR database at once. The tool seems to work alright, except when
> I try to enter multiple fasta sequences in one go. It analyzes/writes
> only the first seq and then exits with:
>
>     EMBOSS An error in jaspscan.c at line 763:
> Cannot open matrix file <null>
>
> I could maybe write a script that feeds sequences one after one, but
> I'd like to do it the cleaner way.
>
> Now, since I am very new to EMBOSS, I might be doing something very
> obvious wrong. Basically I do:
> $ jaspscan
> Scans DNA sequences for transcription factors
> Input nucleotide sequence(s): test?.seq
> Jaspar matrix set
>           C : Core
>           F : Fam
>           P : Phylofacts
>           N : CNE
>           O : POLII
>           S : SPLICE
> Matrix set [C]:
> Comma separated matrix list [all]:
> Threshold percentage [80.0]:
> Output report [fasta_test.jaspscan]:
>
> And I have two files called test1.seq and test2.seq, which are both
> fasta formatted files. Each one can be analyzed in a single-file
> session, but there seems to be an error when processing the two of
> them. If anyone has an idea how to get this working I'd love to hear it.
>
> Cheers,
> jorrit
>
>
> --
> Jorrit Boekel
>
> Ph.D. student
> Dept. of Neuroscience
> Karolinska Institutet
>
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>
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From mathog at caltech.edu  Mon Aug  4 17:39:36 2008
From: mathog at caltech.edu (David Mathog)
Date: Mon, 04 Aug 2008 10:39:36 -0700
Subject: [EMBOSS] how string is shuffleseq
Message-ID: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>

> Not a direct answer to your question - but there was an interesting 
> paper on shuffling recently, did you see it:
> 
> Jiang et al. (2008) uShuffle: A useful tool for shuffling biological 
> sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.

An even less direct answer - I finally got around to rewriting and
generalizing my make_random_dna program from GCG/Fortran to
make_random_seq in standard C, with a GPL 2 license.  So now I can
finally distribute it, instead of having to tell people who ask for it
they can't have it because of licensing issues. 

This program does not maintain the tuple ratios exactly as would (some)
shuffle programs, but it comes arbitrarily close to doing so on a long
enough generated sequence.   It is normally used to generate control
sequences for other programs, as are the various shuffle programs.  The
original would only do DNA, the new one will do DNA, protein, ASCII, or
any specified subset of ASCII.  

It is available here:

http://saf.bio.caltech.edu/pub/software/molbio/make_random_seq.c

Regards,

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


From Jorrit.Boekel at ki.se  Tue Aug  5 09:01:48 2008
From: Jorrit.Boekel at ki.se (Jorrit Boekel)
Date: Tue, 5 Aug 2008 11:01:48 +0200
Subject: [EMBOSS] jaspscan - multiple sequences
In-Reply-To: <56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>
References: <0320858A-1C63-456D-8A7F-32DCE8B2EF1B@ki.se>
	<56815.86.9.126.186.1217865032.squirrel@webmail.ebi.ac.uk>
Message-ID: <7D30B26E-1E99-4C53-97D9-B8FC64C5964A@ki.se>

Hi,

Thanks for the patch! Works like a charm.

jorrit

On Aug 4, 2008, at 5:50 PM, ajb at ebi.ac.uk wrote:

> Dear Jorrit,
>
> It was an oversight. The attached patch file should fix the
> source code - it was created a while ago to help someone who
> asked the same question. Go into the EMBOSS-6.0.1 directory and type:
>
> gunzip -c /somewhere/jaspscan-patch.gz | patch -p1
>
>
> then recompile. I am away at the moment but one of my colleagues  
> will be
> able to answer any further questions on this. The attached will become
> part of an official patch sometime after I get back.
>
> Alan
>
>
>> Dear all,
>>
>> I have only today found and installed EMBOSS on an OSX10.4 computer,
>> because I wanted to use jaspscan to feed multiple sequences to the
>> JASPAR database at once. The tool seems to work alright, except when
>> I try to enter multiple fasta sequences in one go. It analyzes/writes
>> only the first seq and then exits with:
>>
>>     EMBOSS An error in jaspscan.c at line 763:
>> Cannot open matrix file <null>
>>
>> I could maybe write a script that feeds sequences one after one, but
>> I'd like to do it the cleaner way.
>>
>> Now, since I am very new to EMBOSS, I might be doing something very
>> obvious wrong. Basically I do:
>> $ jaspscan
>> Scans DNA sequences for transcription factors
>> Input nucleotide sequence(s): test?.seq
>> Jaspar matrix set
>>           C : Core
>>           F : Fam
>>           P : Phylofacts
>>           N : CNE
>>           O : POLII
>>           S : SPLICE
>> Matrix set [C]:
>> Comma separated matrix list [all]:
>> Threshold percentage [80.0]:
>> Output report [fasta_test.jaspscan]:
>>
>> And I have two files called test1.seq and test2.seq, which are both
>> fasta formatted files. Each one can be analyzed in a single-file
>> session, but there seems to be an error when processing the two of
>> them. If anyone has an idea how to get this working I'd love to  
>> hear it.
>>
>> Cheers,
>> jorrit
>>
>>
>> --
>> Jorrit Boekel
>>
>> Ph.D. student
>> Dept. of Neuroscience
>> Karolinska Institutet
>>
>>
>>
>>
>> _______________________________________________
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/emboss
>>
>> <jaspscan-patch.gz>



From peter.robinson at t-online.de  Tue Aug  5 09:50:51 2008
From: peter.robinson at t-online.de (Peter Robinson)
Date: Tue, 05 Aug 2008 11:50:51 +0200
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
 cannot open shared object file: No such file or directory
Message-ID: <4898227B.2000000@t-online.de>

Hi all,

I have tried to install EMBOSS 6.0 and got through ./configure, make, 
make install without error messages. However, when I try to start an 
emboss program, I get the following error:

error while loading shared libraries: libnucleus.so.6: cannot open 
shared object file: No such file or directory


I am running debian 4.0 & couldnt find any reference to this in google 
or the online docs. Any hints greatly appreciated!
-Peter



From charles-listes-emboss at plessy.org  Tue Aug  5 10:24:18 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Tue, 5 Aug 2008 19:24:18 +0900
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
	cannot open shared object file: No such file or directory
In-Reply-To: <4898227B.2000000@t-online.de>
References: <4898227B.2000000@t-online.de>
Message-ID: <20080805102418.GC12378@kunpuu.plessy.org>

Le Tue, Aug 05, 2008 at 11:50:51AM +0200, Peter Robinson a ?crit :
> 
> I have tried to install EMBOSS 6.0 and got through ./configure, make, 
> make install without error messages. However, when I try to start an 
> emboss program, I get the following error:
> 
> error while loading shared libraries: libnucleus.so.6: cannot open 
> shared object file: No such file or directory
> 
> I am running debian 4.0 & couldnt find any reference to this in google 
> or the online docs. Any hints greatly appreciated!

Hello Peter,

There are now Debian EMBOSS packages version 6.0.1 that can solve your
problem:

http://packages.debian.org/source/experimental/emboss

(The Jaspar patch sent earlier on this list is not yet applied, but will
be soon after it is posted on the EMBOSS FTP site).

Otherwise, you may collect a few more informations to better understand
your problem, with the following commands:

 - which seqret
 - ldd $(which seqret) | grep nucleus
 - ls -l $(ldd $(which seqret) | grep nucleus | cut -f3 -d' ')

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan


From shrish at ccmb.res.in  Tue Aug  5 09:54:32 2008
From: shrish at ccmb.res.in (Shrish Tiwari)
Date: Tue, 5 Aug 2008 15:24:32 +0530 (IST)
Subject: [EMBOSS] Fw:  requests for backtranseq
Message-ID: <143321688.1217930072219.JavaMail.root@127.0.0.1>

An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20080805/25fec8a2/attachment.ksh>

From peter.robinson at t-online.de  Wed Aug  6 07:39:39 2008
From: peter.robinson at t-online.de (Peter Robinson)
Date: Wed, 06 Aug 2008 09:39:39 +0200
Subject: [EMBOSS] error while loading shared libraries: libnucleus.so.6:
 cannot open shared object file: No such file or directory
In-Reply-To: <20080805102418.GC12378@kunpuu.plessy.org>
References: <4898227B.2000000@t-online.de>
	<20080805102418.GC12378@kunpuu.plessy.org>
Message-ID: <4899553B.1070704@t-online.de>

Charles Plessy wrote:
> Le Tue, Aug 05, 2008 at 11:50:51AM +0200, Peter Robinson a ?crit :
>   
>> I have tried to install EMBOSS 6.0 and got through ./configure, make, 
>> make install without error messages. However, when I try to start an 
>> emboss program, I get the following error:
>>
>> error while loading shared libraries: libnucleus.so.6: cannot open 
>> shared object file: No such file or directory
>>
>> I am running debian 4.0 & couldnt find any reference to this in google 
>> or the online docs. Any hints greatly appreciated!
>>     
>
>   





> Hello Peter,
>
> There are now Debian EMBOSS packages version 6.0.1 that can solve your
> problem:
>
> http://packages.debian.org/source/experimental/emboss
>
> (The Jaspar patch sent earlier on this list is not yet applied, but will
> be soon after it is posted on the EMBOSS FTP site).
>
> Otherwise, you may collect a few more informations to better understand
> your problem, with the following commands:
>
>  - which seqret
>  - ldd $(which seqret) | grep nucleus
>  - ls -l $(ldd $(which seqret) | grep nucleus | cut -f3 -d' ')
>
> Have a nice day,
>
>   
Hi Charles,

I want to use the emboss-ized PHYLIP programs, which do not seem to be 
in the debian package (the 5.0 package that is in testing).  I figured 
out what the problem is and am posting it here in case anybody else runs 
across the same problem.

1) The output of ldd $(which seqret) was:

peter at peter:~$ which seqret
/usr/local/bin/seqret
peter at peter:~$ seqret
seqret: error while loading shared libraries: libnucleus.so.6: cannot 
open shared object file: No such file or directory
peter at peter:~$ ldd $(which seqret)
        linux-gate.so.1 =>  (0xb7efc000)
        libnucleus.so.6 => not found
        libajaxg.so.6 => not found
        libajax.so.6 => not found
        libeplplot.so.3 => not found
        libX11.so.6 => /usr/lib/libX11.so.6 (0xb7deb000)
        libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7dc5000)
        libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7c6a000)
        libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb7c67000)
        libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7c4f000)
        libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb7c4b000)
        /lib/ld-linux.so.2 (0xb7efd000)
        libXau.so.6 => /usr/lib/libXau.so.6 (0xb7c48000)
        libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7c43000)

2) I therefore was missing the shared library for plplot, which had 
apparently prevented the nucleus and ajax libraries from being properly 
installed. I installed the libplplot-dev debian package and went through 
configure-make-make install for EMBOSS-6.0.1 and PHYLIP and now 
everything works.

-thanks, Peter




From d.gatherer at mrcvu.gla.ac.uk  Thu Aug  7 14:50:55 2008
From: d.gatherer at mrcvu.gla.ac.uk (Derek Gatherer)
Date: Thu, 07 Aug 2008 15:50:55 +0100
Subject: [EMBOSS] how strong is shuffleseq (Summary)
In-Reply-To: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>
References: <E1KQ41w-0004Pw-00@mendel.bio.caltech.edu>
Message-ID: <E1KR6pU-0001E3-00@hillhead.cent.gla.ac.uk>

Thanks to those who replied.

I compared shuffleseq with make_randon_dna (the latter with flags: -n 
-order 1).

The test was a piece of software that recognises certain complex 
patterns within genomes.  As controls for that pattern recognition 
process, the genomes were iteratively shuffled 100 times with both 
the shuffling applications (by iteratively I mean shuffle once then 
pipe the output back in to re-shuffle and so on).

There seemed to be no difference in the background scores for 
shuffling once, 10 times etc up to 100 times.  I therefore infer that 
the slight background rate that was troubling me is not an artefact 
of poor shuffing.

Therefore, the answer to the original question, I reckon, is: 
shuffleseq is just as good if you choose to shuffle once as to 
shuffle 100 times.  The same is true for make_randon_dna.  There is 
nothing to separate the two programs in performance.

D.



From mathog at caltech.edu  Thu Aug  7 19:29:35 2008
From: mathog at caltech.edu (David Mathog)
Date: Thu, 07 Aug 2008 12:29:35 -0700
Subject: [EMBOSS] how strong is shuffleseq (Summary)
Message-ID: <E1KRBB1-0006bq-Cf@mendel.bio.caltech.edu>

Derek Gatherer wrote:
> Therefore, the answer to the original question, I reckon, is: 
> shuffleseq is just as good if you choose to shuffle once as to 
> shuffle 100 times. The same is true for make_randon_dna.  

Actually, running make_random_seq twice in a row to generate a single
sequence is actually counterproductive.  If you do that the first run
will have a transition table which exactly matches those in the input
sequence, while the second run will generate a transition table from the
first randomized sequence, and since that is of finite length, the
second run will only obtain an approximation of the originally observed
transition frequencies for use in generating the final randomized
sequence.  The shorter the sequence, the greater this effect will be. 

>  There is 
> nothing to separate the two programs in performance.

The two randomized sequences should have slightly different properties. 

The output of shuffleseq will maintain composition (exactly), while the
output of make_random_seq, with the parameters you used, will maintain
dimer composition (approximately).  How different the random sequences
produced  by the two programs are will depend to a great extent on how
skewed the dimer composition of the input sequence was with respect to
the expected dimer composition (as calculated from the monomer
composition).  That is, if A,G,C,T are all 25%, and all dimers are
6.25%, the outputs of the two programs would be very similar.  However,
consider an extreme case which illustrates how much they can differ:

% echo AGCTAGCTAGCTAGCT \
  | make_random_seq -in - -inproc 2 -order 1 -n
>random_sequence_0
TAGCTAGCTAGCTAGC

Which is just the original sequence (phase shifted).  Similarly, for
this very short sequence, even -order 0 would be distinguishable:

% echo AGCTAGCTAGCTAGCT | make_random_seq -in - -inproc 2 -order 0 -n  
>random_sequence_0
GAAAGACTCTGTATGG

In this case resulting in a sequence with 5 G, 5 A, 4 T, 2 C, whereas
shuffleseq would still have exactly 4 of each.

Regards,

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


From john.walshaw at bbsrc.ac.uk  Mon Aug 18 17:37:50 2008
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Mon, 18 Aug 2008 18:37:50 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
Message-ID: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>

Hello,
 
I'm having trouble getting seqret to return the expected FASTA-header
style when using the 'ncbi' output sequence format, when applying it to
either the native UniProt data files or an EMBOSS database made from
them.
 
In the manual for seqret, in the section "Output Format...", this is the
description of the "ncbi" style of FASTA format:
 
ncbi multiple NCBI style FASTA format with the database name, entry
   name and accession number separated by pipe ("|") characters.

 
When I apply seqret to the current native-format UniProt files (Jul
22nd,UniProt release 14.0) with these arguments I get the following
FASTA-format headers:
 
seqret uniprot_sprot.dat -outseq stdout -osf ncbi | grep '^>' | head -5

 
>gnl|unk|104K_THEAN (Q4U9M9) RecName: Full=104 kDa microneme/rhoptry
antigen; AltName: Full=p104; Flags: Precursor;
>gnl|unk|104K_THEPA (P15711) RecName: Full=104 kDa microneme/rhoptry
antigen; AltName: Full=p104; Flags: Precursor;
>gnl|unk|108_SOLLC (Q43495) RecName: Full=Protein 108; Flags: Precursor;
>gnl|unk|10KD_VIGUN (P18646) RecName: Full=10 kDa protein; AltName:
Full=Clone PSAS10; Flags: Precursor;
>gnl|unk|110KD_PLAKN (P13813) RecName: Full=110 kDa antigen; AltName:
Full=PK110; Flags: Fragment;

- shouldn't this be something like this instead:
 
>unk|104K_THEAN|Q4U9M9  .....
>unk|104K_THEPA|P15711 ....
 
etc?
 
seqret seems to be identifying the ID and AccNo separately ok, because
if I specify 'fasta' or 'pearson' as the output format I get the
expected headers, i.e.:
 
>104K_THEAN Q4U9M9 RecName: Full=104 kDa microneme/rhoptry antigen;
AltName: Full=p104; Flags: Precursor;
 
etc.
 
I've found this behaviour in EMBOSS 5.0.0 and 6.0.1. If I apply seqret
to an EMBOSS database I've made by running dbxflat on the native UniProt
files, then -osf ncbi gives me the same format as when applied directly
to the files, except that the database name appears instead of 'unk'.
 
By the way, is there a way of making seqret return the same style header
as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
>db|id|accno), or is this what the ncbi format is intended to do?
 
best wishes,
 
Dr John Walshaw
Department of Computational & Systems Biology
John Innes Centre
Colney
Norwich NR4 7UH
UK
 
 



From emno72 at gmail.com  Tue Aug 19 03:06:46 2008
From: emno72 at gmail.com (Mohd Noor Mat Isa)
Date: Tue, 19 Aug 2008 11:06:46 +0800
Subject: [EMBOSS] EMBOSS 6 on SuSe SLES 10 ia64
Message-ID: <2e2159f50808182006u56b9f101v1042af4d820871be@mail.gmail.com>

Hi all,
I try to compile the EMBOSS 6 on my Itanium 2 server (SGI Altix4700) running
SuSe SLES 10. No errors are found during the compilation process... but I
can't run it. The error message as below:

"error while loading shared libraries: libnucleus.so.6: cannot open shared
object file: No such file or directory"

this is the report once I run ldd:

Altix4700:/home/emno # ldd $(which seqret)
        linux-gate.so.1 =>  (0xa000000000000000)
        libnucleus.so.6 => not found
        libajaxg.so.6 => not found
        libajax.so.6 => not found
        libeplplot.so.3 => not found
        libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x2000000000064000)
        libm.so.6.1 => /lib/libm.so.6.1 (0x2000000000238000)
        libc.so.6.1 => /lib/libc.so.6.1 (0x2000000000308000)
        libdl.so.2 => /lib/libdl.so.2 (0x2000000000558000)
        /lib/ld-linux-ia64.so.2 (0x2000000000000000)
Altix4700:/home/emno #

I try to find plplot rpm for suse ia64 to get this library but could not
find it .. anybody can help or give any sugestions

Thanks
Mohd Noor


From pmr at ebi.ac.uk  Tue Aug 19 08:29:46 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 19 Aug 2008 09:29:46 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
Message-ID: <48AA847A.2070808@ebi.ac.uk>

john walshaw (JIC) wrote:
  > I'm having trouble getting seqret to return the expected FASTA-header
> style when using the 'ncbi' output sequence format, when applying it to
> either the native UniProt data files or an EMBOSS database made from
> them.
>  
> In the manual for seqret, in the section "Output Format...", this is the
> description of the "ncbi" style of FASTA format:
>  
> ncbi multiple NCBI style FASTA format with the database name, entry
>    name and accession number separated by pipe ("|") characters.

This could be extended to explain that NCBI also have an annoyingly 
short list of valid database names. Any other name has to appear as 
"gnl|dbname", as you see for your uniprox database indexd with dbxflat. 
We use "unk" if we have no known database name, but we treat it as a 
general name - NCBI's "unk|identifier" is something special to them.

If you use one of the "NCBI list" database names, for example adding 
"-sdbname sp" to the command line, you will get a swissprot NCBI sandard 
identifier - but this is because "sp" is one of their special names. You 
cannot even assume the data is protein if you see "sp" in the identifier 
(genpept for example uses emb and gb as database names for protein 
sequences).

> By the way, is there a way of making seqret return the same style header
> as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
>> db|id|accno), or is this what the ncbi format is intended to do?

Hmmmm .... yet another FASTA format (and see below for another one). 
Yes, that looks like a good idea. We need an output name for it, perhaps 
wublast is the best choice.

You emntioned UniProt 14 - the latest release also includes extensions 
to the Fasta format description to tag species and other information. We 
are considering making this the default version of the FASTA format for 
EMBOSS so we can preserve more information - does this sound like a good 
idea?

For example: >sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry antigen 
OS=Theileria annulata GN=TA08425 PE=3 SV=1


Also on the subject of UniProt 14 - the .dat flat files have a new 
syntax for the DE lines. we had to ignore that as the cange appeared 
just before EMBOSS 6.0.0 Is anyone interested in having the details 
parsed out, or in having the original friendly description generated?

ID   104K_THEAN              Reviewed;         893 AA.
AC   Q4U9M9;
DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2005, sequence version 1.
DT   22-JUL-2008, entry version 18.
DE   RecName: Full=104 kDa microneme/rhoptry antigen;
DE   AltName: Full=p104;
DE   Flags: Precursor;

Hope this helps, even if it adds some new questions!

Peter


From john.walshaw at bbsrc.ac.uk  Tue Aug 19 09:25:36 2008
From: john.walshaw at bbsrc.ac.uk (john walshaw (JIC))
Date: Tue, 19 Aug 2008 10:25:36 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <48AA847A.2070808@ebi.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
	<48AA847A.2070808@ebi.ac.uk>
Message-ID: <E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>


Thanks for your help Peter, please see comments below. 

> -----Original Message-----
> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
> Sent: 19 August 2008 09:30
> To: john walshaw (JIC)
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] seqret output sequence format "ncbi"
> 
> john walshaw (JIC) wrote:
>   > I'm having trouble getting seqret to return the expected 
> FASTA-header
> > style when using the 'ncbi' output sequence format, when 
> applying it 
> > to either the native UniProt data files or an EMBOSS database made 
> > from them.
> >  
> > In the manual for seqret, in the section "Output 
> Format...", this is 
> > the description of the "ncbi" style of FASTA format:
> >  
> > ncbi multiple NCBI style FASTA format with the database name, entry
> >    name and accession number separated by pipe ("|") characters.
> 
> This could be extended to explain that NCBI also have an 
> annoyingly short list of valid database names. Any other name 
> has to appear as "gnl|dbname", as you see for your uniprox 
> database indexd with dbxflat. 
> We use "unk" if we have no known database name, but we treat 
> it as a general name - NCBI's "unk|identifier" is something 
> special to them.
> 
> If you use one of the "NCBI list" database names, for example 
> adding "-sdbname sp" to the command line, you will get a 
> swissprot NCBI sandard identifier - but this is because "sp" 
> is one of their special names. You cannot even assume the 
> data is protein if you see "sp" in the identifier (genpept 
> for example uses emb and gb as database names for protein sequences).
> 

Thanks, I see, that does it. So if I had named my database 'sp' instead
of 'uniprot' this would have worked automatically. 

> > By the way, is there a way of making seqret return the same style 
> > header as WU-BLAST sp2fasta, i.e. >db|accno|id  ....  (instead of
> >> db|id|accno), or is this what the ncbi format is intended to do?
> 
> Hmmmm .... yet another FASTA format (and see below for another one). 
> Yes, that looks like a good idea. We need an output name for 
> it, perhaps wublast is the best choice.
> 

BTW the reason I ask this is that sp2fasta doesn't seem able to handle
the format changes in the DE line which have appeared in release 14.0.
My theory is that the format change, re below, occasionally makes
some DE lines very long, and too long for sp2fasta to read, so the
final continuation character (semicolon) is missed. This means that
if the next line is also a DE line, sp2fasta halts with a fatal error
about there being multiple definition lines for one sequence record.
Examples in release 14.0 are Q5IGR8 (in uniprot_sprot.dat) and A0B5I3
(in uniprot_trembl.dat). If there's a v. long DE line but the next
line isn't a DE line, then it doesn't matter and sp2fasta is ok.

> You emntioned UniProt 14 - the latest release also includes 
> extensions to the Fasta format description to tag species and 
> other information. We are considering making this the default 
> version of the FASTA format for EMBOSS so we can preserve 
> more information - does this sound like a good idea?
> 
> For example: >sp|Q4U9M9|104K_THEAN 104 kDa microneme/rhoptry 
> antigen OS=Theileria annulata GN=TA08425 PE=3 SV=1
> 

Personally, I think this would be a good idea. I'm assuming that
EMBOSS progs would themselves be able to parse these fields from the
FASTA headers?

> 
> Also on the subject of UniProt 14 - the .dat flat files have a new 
> syntax for the DE lines. we had to ignore that as the cange appeared 
> just before EMBOSS 6.0.0 Is anyone interested in having the details 
> parsed out, or in having the original friendly description generated?
> 
> ID   104K_THEAN              Reviewed;         893 AA.
> AC   Q4U9M9;
> DT   18-APR-2006, integrated into UniProtKB/Swiss-Prot.
> DT   05-JUL-2005, sequence version 1.
> DT   22-JUL-2008, entry version 18.
> DE   RecName: Full=104 kDa microneme/rhoptry antigen;
> DE   AltName: Full=p104;
> DE   Flags: Precursor;

Having the option to parse them out would be useful :) These multiple
names can be a bit awkward sometimes, so if UniProt and EMBOSS do some
of the work for you, that's got to be good.

> 
> Hope this helps, even if it adds some new questions!
> 

Certainly does, many thanks again.

cheers

John

> Peter
> 



From pmr at ebi.ac.uk  Tue Aug 19 09:52:42 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Tue, 19 Aug 2008 10:52:42 +0100
Subject: [EMBOSS] seqret output sequence format "ncbi"
In-Reply-To: <E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>
References: <E15BDDABACA8AB409BCC1071AC790DCB03A098AD@NBIE2KSRV1.nbi.bbsrc.ac.uk>
	<48AA847A.2070808@ebi.ac.uk>
	<E15BDDABACA8AB409BCC1071AC790DCB03A098AE@NBIE2KSRV1.nbi.bbsrc.ac.uk>
Message-ID: <48AA97EA.4090106@ebi.ac.uk>

john walshaw (JIC) wrote:
> Thanks for your help Peter, please see comments below. 
>> From: Peter Rice [mailto:pmr at ebi.ac.uk] 
>> Sent: 19 August 2008 09:30
>> You emntioned UniProt 14 - the latest release also includes 
>> extensions to the Fasta format description to tag species and 
>> other information. We are considering making this the default 
>> version of the FASTA format for EMBOSS so we can preserve 
>> more information - does this sound like a good idea?
> 
> Personally, I think this would be a good idea. I'm assuming that
> EMBOSS progs would themselves be able to parse these fields from the
> FASTA headers?

Yes ... assuming they fit the expected format. We have to hope that no
other "FASTA" format is using something similar. UniProt has a very
limited set of XX= tags - depending on which part of UniProt you look at.

>> Also on the subject of UniProt 14 - the .dat flat files have a new 
>> syntax for the DE lines. we had to ignore that as the cange appeared 
>> just before EMBOSS 6.0.0 Is anyone interested in having the details 
>> parsed out, or in having the original friendly description generated?
> 
> Having the option to parse them out would be useful :) These multiple
> names can be a bit awkward sometimes, so if UniProt and EMBOSS do some
> of the work for you, that's got to be good.

Thanks. We will try to parse them. If we can generate the equivalent
UniProt 13 descriptions then we will know we have a reasonable parser.

If we can parse them ... my preference would be to use the old-style
descriptions. Only UniProt seems to be using this new split in their 
releases.

regards,

Peter



From dalloliogm at gmail.com  Wed Aug 20 08:17:26 2008
From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio)
Date: Wed, 20 Aug 2008 10:17:26 +0200
Subject: [EMBOSS] SeaView
In-Reply-To: <C4A53ED6.A492%staffa@niehs.nih.gov>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
Message-ID: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>

On Fri, Jul 18, 2008 at 12:24 AM, Staffa, Nick (NIH/NIEHS) <
staffa at niehs.nih.gov> wrote:

>
> I would really appreciate any evaluation of the editor SEAVIEW by anyone
> reading this. In reading the paper by Galtier,Gouy and Gautier,
>


Hi all,
I thought this discussion was so interesting, that I have opened a section
in wikipedia to discuss all sequence alignment editor software, starting
from those that you have described here.

Can you please have a look at this link:
-
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Alignment_Viewers.2FEditors
and tell me if it is ok, or if you have more suggestions.

I was thinking I could also put mega[1] as a sequence alignment editor
program. In fact, with this software you can edit alignments, even if the
program is made for making phylogenetics analysis.
What do you think?


[1] http://www.megasoftware.net/


>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Enterprise-Wide Information Technology Support Contract
> (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



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

My Blog on Bioinformatics (italian): http://bioinfoblog.it


From gbottu at vub.ac.be  Wed Aug 20 08:59:51 2008
From: gbottu at vub.ac.be (Guy Bottu)
Date: Wed, 20 Aug 2008 10:59:51 +0200
Subject: [EMBOSS] SeaView
In-Reply-To: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
	<5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
Message-ID: <48ABDD07.1000307@vub.ac.be>

Giovanni Marco Dall'Olio wrote:
> I thought this discussion was so interesting, that I have opened a section
> in wikipedia to discuss all sequence alignment editor software, starting
> from those that you have described here.

Nice initative !

A remark : the latest version of SeaView I have seen supports clustalw and 
muscle for re-alignment, not t-coffee (although you can re-configure SeaView to 
put any alignment software in).

Some other software that could be mentioned :
- Genedoc (very useful for preparing alignments for publication)
   http://www.nrbsc.org/gfx/genedoc

- SeqPup
   http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/

- MSE (text-mode, also embossified version available as Embassy package)

	Regards,
	Guy Bottu,
	BEN



From staffa at niehs.nih.gov  Wed Aug 20 14:11:13 2008
From: staffa at niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C])
Date: Wed, 20 Aug 2008 10:11:13 -0400
Subject: [EMBOSS] SeaView
In-Reply-To: <5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
References: <487F0F89.7030402@genomics.dk> <C4A53ED6.A492%staffa@niehs.nih.gov>
	<5aa3b3570808200117i325ba304ge8369ab4d585e338@mail.gmail.com>
Message-ID: <7930EE6CD7CA354D93B444D0433C0611068488EB@NIHCESMLBX6.nih.gov>

It's nice to know, for once, who the author of a Wikipedia article is.

Nickolas G. Staffa, Jr. Ph.D.
Telephone: 919-316-4569  (NIEHS: 6-4569) 
Scientific Computing Support Group
NIEHS E-WITS Contract 
Science Task Monitor: Roy W. Reter ( reter at niehs.nih.gov )
National Institute of Environmental Health Sciences 
National Institutes of Health 
Research Triangle Park, North Carolina
 

-----Original Message-----
From: Giovanni Marco Dall'Olio [mailto:dalloliogm at gmail.com] 
Sent: Wednesday, August 20, 2008 4:17 AM
To: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] SeaView

On Fri, Jul 18, 2008 at 12:24 AM, Staffa, Nick (NIH/NIEHS) <
staffa at niehs.nih.gov> wrote:

>
> I would really appreciate any evaluation of the editor SEAVIEW by
anyone
> reading this. In reading the paper by Galtier,Gouy and Gautier,
>


Hi all,
I thought this discussion was so interesting, that I have opened a
section
in wikipedia to discuss all sequence alignment editor software, starting
from those that you have described here.

Can you please have a look at this link:
-
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Alignme
nt_Viewers.2FEditors
and tell me if it is ok, or if you have more suggestions.

I was thinking I could also put mega[1] as a sequence alignment editor
program. In fact, with this software you can edit alignments, even if
the
program is made for making phylogenetics analysis.
What do you think?


[1] http://www.megasoftware.net/


>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Enterprise-Wide Information Technology Support Contract
> (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



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

My Blog on Bioinformatics (italian): http://bioinfoblog.it
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss



From marcusclaesson at gmail.com  Tue Aug 26 10:07:04 2008
From: marcusclaesson at gmail.com (Marcus Claesson)
Date: Tue, 26 Aug 2008 12:07:04 +0200
Subject: [EMBOSS] can vectorstrip deal with indels?
Message-ID: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>

Hi,

According to the docs of vectorstrip it has a mismatch parameter which sets
the max allowed mismatch as a percentage. However, my input sequences
sometimes contain not just a mismatched character, but also a nucletide
insertion/deletion. It seems like vectorstrip can't handle this. Is this
correct or is there a way to introduce indels as well?

Many thanks,
Marcus


From ajb at ebi.ac.uk  Wed Aug 27 08:33:10 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Wed, 27 Aug 2008 09:33:10 +0100 (BST)
Subject: [EMBOSS] First 6.0.1 fixes available
Message-ID: <55051.86.9.126.186.1219825990.squirrel@webmail.ebi.ac.uk>

Some fixes are now available on the ftp server for EMBOSS 6.0.1 in
the usual places (for UNIX users):

ftp://emboss.open-bio.org/pub/EMBOSS/fixes/
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/

For most sites, using the 'patches' method will be the most
convenient (read the README in that directory).

The fixes are:

Fix 1. EMBOSS-6.0.1/emboss/jaspscan.c
       EMBOSS-6.0.1/nucleus/embprop.c

26 Aug 2008: jaspscan can now scan multiple sequences.
             "digest -allpartials" now reports all C-term fragments


For mEMBOSS (Windows) users the following setup file is a replacement
for the main release (6.0.1) and contains the above fixes. It
is constructed from the CVS code and so has 'beta' status. This file
also contains some fixes to the GUI. It also contains applications,
new to EMBOSS 6, which were in the UNIX version but didn't make it
into the mEMBOSS 6.0.1 release. You should uninstall any
current mEMBOSS installation before installing any new setup file.

ftp://emboss.open-bio.org/pub/EMBOSS/windows/beta/mEMBOSS-6.0.1.1-setup.exe


Alan




From pmr at ebi.ac.uk  Wed Aug 27 10:36:13 2008
From: pmr at ebi.ac.uk (Peter Rice)
Date: Wed, 27 Aug 2008 11:36:13 +0100
Subject: [EMBOSS] can vectorstrip deal with indels?
In-Reply-To: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>
References: <d939c600808260307v43f0ae92ifb071661a794be4a@mail.gmail.com>
Message-ID: <48B52E1D.9070808@ebi.ac.uk>

Marcus Claesson wrote:
> Hi,
> 
> According to the docs of vectorstrip it has a mismatch parameter which sets
> the max allowed mismatch as a percentage. However, my input sequences
> sometimes contain not just a mismatched character, but also a nucleotide
> insertion/deletion. It seems like vectorstrip can't handle this. Is this
> correct or is there a way to introduce indels as well?

Vectorstrip uses the EMBOSS pattern matching routines. These support
mismatches but not indels.

One possibility is to modify vectorstrip to define all possible indels
in the linker sequences. We can look into the performance impact.

Thanks for the sugestion

Peter Rice


From golharam at umdnj.edu  Sat Aug 23 18:33:17 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 23 Aug 2008 14:33:17 -0400
Subject: [EMBOSS] DOMAINATRIX compile error
Message-ID: <48B057ED.6000104@umdnj.edu>

So I''ve finally got around to building RPMs for EMBOSS 6.0.1 on RHEL5. 
  I got EMBOSS to build just fine and the RPMs look good.

Now, I'm working on building the EMBASSY packages.  I started with 
DOMAINATRIX and ran into a compiler error:

domainreso.c: In function ?main?:
domainreso.c:150: warning: ?ajFileNewIn? is deprecated (declared at 
/usr/include/ajfile.h:461)
domainseqs.c: In function ?main?:
domainseqs.c:176: warning: ?ajFileNewDirF? is deprecated (declared at 
/usr/include/ajfile.h:507)
domainseqs.c:180: warning: ?ajDirExt? is deprecated (declared at 
/usr/include/ajfile.h:453)
domainseqs.c: In function ?domainseqs_AlignDomain?:
domainseqs.c:485: warning: passing argument 12 of ?embAlignWalkNWMatrix? 
from incompatible pointer type
domainseqs.c:485: error: too many arguments to function 
?embAlignWalkNWMatrix?
make[2]: *** [domainseqs.o] Error 1


Any ideas?

Ryan


From golharam at umdnj.edu  Sat Aug 23 18:41:59 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Sat, 23 Aug 2008 14:41:59 -0400
Subject: [EMBOSS] DOMAINATRIX compile error
In-Reply-To: <48B057ED.6000104@umdnj.edu>
References: <48B057ED.6000104@umdnj.edu>
Message-ID: <48B059F7.1060302@umdnj.edu>

Ignore my message.  I didn't move the new tarball in place when 
rebuilding.

Ryan Golhar wrote:
> So I''ve finally got around to building RPMs for EMBOSS 6.0.1 on RHEL5. 
>  I got EMBOSS to build just fine and the RPMs look good.
> 
> Now, I'm working on building the EMBASSY packages.  I started with 
> DOMAINATRIX and ran into a compiler error:
> 
> domainreso.c: In function ?main?:
> domainreso.c:150: warning: ?ajFileNewIn? is deprecated (declared at 
> /usr/include/ajfile.h:461)
> domainseqs.c: In function ?main?:
> domainseqs.c:176: warning: ?ajFileNewDirF? is deprecated (declared at 
> /usr/include/ajfile.h:507)
> domainseqs.c:180: warning: ?ajDirExt? is deprecated (declared at 
> /usr/include/ajfile.h:453)
> domainseqs.c: In function ?domainseqs_AlignDomain?:
> domainseqs.c:485: warning: passing argument 12 of ?embAlignWalkNWMatrix? 
> from incompatible pointer type
> domainseqs.c:485: error: too many arguments to function 
> ?embAlignWalkNWMatrix?
> make[2]: *** [domainseqs.o] Error 1
> 
> 
> Any ideas?
> 
> Ryan
> 


From charles-listes-emboss at plessy.org  Wed Aug 27 14:05:20 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Wed, 27 Aug 2008 23:05:20 +0900
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
In-Reply-To: <48B059F7.1060302@umdnj.edu>
References: <48B057ED.6000104@umdnj.edu> <48B059F7.1060302@umdnj.edu>
Message-ID: <20080827140520.GC18561@kunpuu.plessy.org>

Le Sat, Aug 23, 2008 at 02:41:59PM -0400, Ryan Golhar a ?crit :
> Ignore my message.  I didn't move the new tarball in place when  
> rebuilding.

Ouch, the contents of the tarballs seem to have been updated while their
version number was left unchanged. We distribute domainatrix and
domalign in Debian, under the version 0.1.0, but older tarballs from the
EMBOSS 5.o release? Do you think that you can increment the version
number of the new ones on the EMBOSS FTP site? Otherwise we will make an
update under a version number like 0.1.0+20071507?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


From golharam at umdnj.edu  Wed Aug 27 14:33:45 2008
From: golharam at umdnj.edu (Ryan Golhar)
Date: Wed, 27 Aug 2008 14:33:45 +0000
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
Message-ID: <287101333-1219847642-cardhu_decombobulator_blackberry.rim.net-1345440591-@bxe104.bisx.prod.on.blackberry>

I agree, the version numbers should be updated, however they never were in the past.  I update the release number of the RPMs to reflect the change.
------Original Message------
From: Charles Plessy
Sender: emboss-bounces at lists.open-bio.org
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Version number of DOMAINATRIX and DOMALIGN.
Sent: Aug 27, 2008 9:05 AM

Le Sat, Aug 23, 2008 at 02:41:59PM -0400, Ryan Golhar a ?crit :
> Ignore my message.  I didn't move the new tarball in place when  
> rebuilding.

Ouch, the contents of the tarballs seem to have been updated while their
version number was left unchanged. We distribute domainatrix and
domalign in Debian, under the version 0.1.0, but older tarballs from the
EMBOSS 5.o release? Do you think that you can increment the version
number of the new ones on the EMBOSS FTP site? Otherwise we will make an
update under a version number like 0.1.0+20071507?

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
_______________________________________________
EMBOSS mailing list
EMBOSS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss


Sent from my Verizon Wireless BlackBerry



From benys at usp.br  Thu Aug 28 23:25:37 2008
From: benys at usp.br (Beny Spira)
Date: Thu, 28 Aug 2008 20:25:37 -0300
Subject: [EMBOSS] jemboss
Message-ID: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>

Hi all
I've been trying to install jemboss as 'standalone' in my laptop. Its OS is
Linux Debian sid. I've previously installed jemboss in a PC running Mandriva
without any problems. But in Debian I get the following message:

------------------------- WARNING ----------------------------

The script has detected that /usr/include/gd.h
does not exist

Download gd from
       http://www.boutell.com/gd/

For details see the EMBOSS admin guide:
http://emboss.sourceforge.net/admin/

To exit use Control C or press return to continue.
-----------------------------------------------------------------------

gd.h is in /usr/include and libpng is also installed, so I don't know what
the problem is.

Any help would be appreciated,
Beny


-- 
Beny Spira
Departamento de Microbiologia
Instituto de Ci?ncias Biom?dicas
Universidade de S?o Paulo
Av. Prof. Lineu Prestes 1374
S?o Paulo-SP CEP:05508-900
Brasil
Tel: 5511-3091-7347
FAX: 5511-3091-7354
E-mail: benys at usp.br
Homepage: www.icb.usp.br/~benys



From ajb at ebi.ac.uk  Fri Aug 29 08:00:03 2008
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Fri, 29 Aug 2008 09:00:03 +0100 (BST)
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
Message-ID: <55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>

Hi,

Looking at the script that message is indeed misleading. It will happen
if the script (in the case of Debian) can't find libgd.so.
I don't have a Debian installation to hand but I believe the
package you need to install is libgd2-dev (Debian users on this list will
correct me if I'm wrong). Installing that package should pull in all other
required dependencies for GD/PNG.

HTH

Alan

> Hi all
> I've been trying to install jemboss as 'standalone' in my laptop. Its OS
> is
> Linux Debian sid. I've previously installed jemboss in a PC running
> Mandriva
> without any problems. But in Debian I get the following message:
>
> ------------------------- WARNING ----------------------------
>
> The script has detected that /usr/include/gd.h
> does not exist
>
> Download gd from
>        http://www.boutell.com/gd/
>
> For details see the EMBOSS admin guide:
> http://emboss.sourceforge.net/admin/
>
> To exit use Control C or press return to continue.
> -----------------------------------------------------------------------
>
> gd.h is in /usr/include and libpng is also installed, so I don't know what
> the problem is.
>
> Any help would be appreciated,
> Beny
>
>
> --
> Beny Spira
> Departamento de Microbiologia
> Instituto de Ci?ncias Biom?dicas
> Universidade de S?o Paulo
> Av. Prof. Lineu Prestes 1374
> S?o Paulo-SP CEP:05508-900
> Brasil
> Tel: 5511-3091-7347
> FAX: 5511-3091-7354
> E-mail: benys at usp.br
> Homepage: www.icb.usp.br/~benys
>
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From charles-listes-emboss at plessy.org  Fri Aug 29 09:08:45 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Fri, 29 Aug 2008 18:08:45 +0900
Subject: [EMBOSS] jemboss
In-Reply-To: <55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
Message-ID: <20080829090845.GG15089@kunpuu.plessy.org>

Le Fri, Aug 29, 2008 at 09:00:03AM +0100, ajb at ebi.ac.uk a ?crit :
> 
> I don't have a Debian installation to hand but I believe the
> package you need to install is libgd2-dev (Debian users on this list will
> correct me if I'm wrong). Installing that package should pull in all other
> required dependencies for GD/PNG.

Hi,

a very useful tool for that kind of situations on Debian systems is
`apt-file':

anx159?~?$ apt-file search include/gd.h
libgd2-noxpm-dev: /usr/include/gd.h
libgd2-xpm-dev: /usr/include/gd.h

There is a very unforunate dichotomy of the GD library on Debian. I
would recommend to use libgd2-xpm-dev unless you really need to have XPM
support disabled.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan


From benys at usp.br  Fri Aug 29 15:21:43 2008
From: benys at usp.br (Beny Spira)
Date: Fri, 29 Aug 2008 12:21:43 -0300
Subject: [EMBOSS] jemboss
In-Reply-To: <20080829090845.GG15089@kunpuu.plessy.org>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
Message-ID: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>

Thanks for the answers. The libgd2-devel package was indeed missing. I
installed libgd2-xpm-dev and jemboss installation went smoothly.
However, I can't run jemboss, there is no response to the command
./runJemboss.sh
I checked the permissions and it is OK.
I even installed the entire EMBOSS package again, but still cannot make it
work.
Any clue what might be wrong?
Beny


On Fri, Aug 29, 2008 at 6:08 AM, Charles Plessy <
charles-listes-emboss at plessy.org> wrote:

> Le Fri, Aug 29, 2008 at 09:00:03AM +0100, ajb at ebi.ac.uk a ?crit :
> >
> > I don't have a Debian installation to hand but I believe the
> > package you need to install is libgd2-dev (Debian users on this list will
> > correct me if I'm wrong). Installing that package should pull in all
> other
> > required dependencies for GD/PNG.
>
> Hi,
>
> a very useful tool for that kind of situations on Debian systems is
> `apt-file':
>
> anx159?~?$ apt-file search include/gd.h
> libgd2-noxpm-dev: /usr/include/gd.h
> libgd2-xpm-dev: /usr/include/gd.h
>
> There is a very unforunate dichotomy of the GD library on Debian. I
> would recommend to use libgd2-xpm-dev unless you really need to have XPM
> support disabled.
>
> Have a nice day,
>
> --
> Charles Plessy
> Debian Med packaging team
> Tsurumi, Kanagawa, Japan
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



-- 
Beny Spira
Departamento de Microbiologia
Instituto de Ci?ncias Biom?dicas
Universidade de S?o Paulo
Av. Prof. Lineu Prestes 1374
S?o Paulo-SP CEP:05508-900
Brasil
Tel: 5511-3091-7347
FAX: 5511-3091-7354
E-mail: benys at usp.br
Homepage: www.icb.usp.br/~benys



From uludag at ebi.ac.uk  Fri Aug 29 18:43:03 2008
From: uludag at ebi.ac.uk (uludag at ebi.ac.uk)
Date: Fri, 29 Aug 2008 19:43:03 +0100 (BST)
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
	<21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
Message-ID: <59214.86.133.34.209.1220035383.squirrel@webmail.ebi.ac.uk>

Hi Beny,

You should have a line something similar to the following in your
runJemboss.sh

   /foo/java org.emboss.jemboss.Jemboss &

Can you try running "/foo/java -version" to check whether your java is
responding?

Is it supplied by Sun?

Jemboss install procedure doesn't automatically add the parameter "local"
to the java command line which is necessary when starting Jemboss in
standalone mode. If you haven't already done it modified command line
should look like

  /foo/java org.emboss.jemboss.Jemboss local &

Regards,
Mahmut

> I can't run jemboss, there is no response to the command
> ./runJemboss.sh
> I checked the permissions and it is OK.
> I even installed the entire EMBOSS package again, but still cannot make it
> work.
> Any clue what might be wrong?
>




From charles-listes-emboss at plessy.org  Sat Aug 30 01:50:14 2008
From: charles-listes-emboss at plessy.org (Charles Plessy)
Date: Sat, 30 Aug 2008 10:50:14 +0900
Subject: [EMBOSS] jemboss
In-Reply-To: <21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
References: <21e884180808281625m6f6fde4ci2932ed82a202c642@mail.gmail.com>
	<55740.86.9.126.186.1219996803.squirrel@webmail.ebi.ac.uk>
	<20080829090845.GG15089@kunpuu.plessy.org>
	<21e884180808290821r4da88fc7p542568a6e3589760@mail.gmail.com>
Message-ID: <20080830015014.GB19735@kunpuu.plessy.org>

Le Fri, Aug 29, 2008 at 12:21:43PM -0300, Beny Spira a ?crit :
> Thanks for the answers. The libgd2-devel package was indeed missing. I
> installed libgd2-xpm-dev and jemboss installation went smoothly.
> However, I can't run jemboss, there is no response to the command
> ./runJemboss.sh
> I checked the permissions and it is OK.
> I even installed the entire EMBOSS package again, but still cannot make it
> work.
> Any clue what might be wrong?

Maybe you forgot to give the path to the jdk when calling the configure
script?

If you use the non-free Sun Java package distributed by Debian (Lenny
release), the following option should do the job:

--with-java=/usr/lib/jvm/java-6-sun-1.6.0.07/include --with-javaos=/usr/lib/jvm/java-6-sun-1.6.0.07/include/linux

The freed version of Sun Java is unfortunately not ready yet, and I do
not know if jemboss works with alternatives (gcj, ...). If it were so,
please contact me, and I will make an official jemboss package for
Debian. If not, we will have to wait for "IcedTea" to be ready.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
Tsurumi, Kanagawa, Japan