From jison at ebi.ac.uk  Mon Apr  4 08:21:42 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Apr 2011 13:21:42 +0100 (BST)
Subject: [EMBOSS] the -orfminsize in SIXPACK and -minsize in GETORF
In-Reply-To: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>
References: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>
Message-ID: <34843.172.22.100.208.1301919702.squirrel@webmail.ebi.ac.uk>

Hi

Didn't see a reply to you.  Anyhow ...


> Are the options -orfminsize in SIXPACK and -minsize in GETORF the same?

Yes (well, they are equivalent).

> Do they both specify "Minimum nucleotide size of ORF to report"?

Yes - we should probably standardise the names of such options.

> Are these two programs supposed to give the same results under identical
> input parameters?

Without looking at the code I'm not sure.  You might expect slight differences depending on how
exactly an ORF is defined.  They should at least broadly agree.

Cheers

Jon



>
> Thanks
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From jison at ebi.ac.uk  Mon Apr  4 08:25:57 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Apr 2011 13:25:57 +0100 (BST)
Subject: [EMBOSS] How to include homing endonucleases?
In-Reply-To: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>
References: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>
Message-ID: <58967.172.22.100.208.1301919957.squirrel@webmail.ebi.ac.uk>

Hi Stefanie

Apologies no reply sooner.

You should use rebaseextract
http://emboss.sourceforge.net/apps/cvs/emboss/apps/rebaseextract.html

Details are in the "Data files" section of the "restrict" docs:
http://emboss.sourceforge.net/apps/cvs/emboss/apps/restrict.html

Cheers

Jon




> Hi,
>
> Rebase got a separate file listing all homing  endonuclease
> (ftp://ftp.neb.com/pub/rebase/homing.103), how can I index that file
> as an alternative to rebase? The Emboss  program restrict have the
> option to use a specific datafile, but it's not clear what format that
> file should be?
>
> Regards,
>
> Stefanie Lager
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>



From a.bruselles at gmail.com  Thu Apr  7 07:27:35 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Thu, 7 Apr 2011 13:27:35 +0200
Subject: [EMBOSS] databases connection failed
Message-ID: <BANLkTimf8JpR8OC=CSa6Xd7z9gp_xFuntA@mail.gmail.com>

Hi all,
I have a problem with the emboss connection with databases;
this is the output (after a while) when I try whichdb or infoseq:
:~$ whichdb BAC1
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Error: socket connect failed for database 'gba'
socket connect failed for database 'gba': Connection timed out
Warning: Cannot open division file '<null>' for database 'emblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trembl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'nbrf'

  EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed

:~$ infoseq genbank:l07770
Display basic information about sequences
Error: socket connect failed for database 'genbank'
socket connect failed for database 'genbank': Connection timed out
Error: Unable to read sequence 'genbank:l07770'
Died: infoseq terminated: Bad value for '-sequence' and no prompt


Does anyone have an idea of what is happening?

thanks

From a.bruselles at gmail.com  Fri Apr  8 06:27:31 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Fri, 8 Apr 2011 12:27:31 +0200
Subject: [EMBOSS] db records retrieve
Message-ID: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>

Hi all,
I'm not able to retrieve sequences starting from official gene symbols (e.g.
BCL2L10),
what db do I have to use?

This is the output of whichdb:

*$ whichdb BCL2L10 -debug
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Warning: Cannot open division file '<null>' for database 'tsw'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'emblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trembl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'nbrf'

   EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed*

Thanks

From pmr at ebi.ac.uk  Fri Apr  8 07:04:52 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 08 Apr 2011 12:04:52 +0100
Subject: [EMBOSS] db records retrieve
In-Reply-To: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
References: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
Message-ID: <4D9EEBD4.8020802@ebi.ac.uk>

On 08/04/2011 11:27, Alessandro Bruselles wrote:
> Hi all,
> I'm not able to retrieve sequences starting from official gene symbols (e.g.
> BCL2L10),
> what db do I have to use?

You need a database you can search by gene name. If the database has 
access through a website you can use the URL access method ... providing 
a URL that returns with the sequence in a format that EMBOSS can read.

For UniProt:

DB uniprotgene [
   type: "protein"
   format: "swiss"
   methodquery: "url"
   url: 
"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-gen:%s]+-ascii"
]

(the URL should be all in one line)

We will have other ways to do this in EMBOSS 6.4.0 when we enable gen 
and other database search fields.

> This is the output of whichdb:
>
> *$ whichdb BCL2L10 -debug
> Search all sequence databases for an entry and retrieve it
> Output file [outfile.whichdb]: stdout
> Warning: Cannot open division file '<null>' for database 'tsw'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'emblnew'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'trembl'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'nbrf'
>
>     EMBOSS An error in ajseqdb.c at line 5350:
> seqCdQryOpen failed*

You need to fix or comment out the tsw, emblnew, trembl and nbrf 
databases to avoid those messages. whichdb tries all sequence databases 
and is a good way to catch database that are not working (servers down, 
data or index files not in the expected directory)

Hope this helps

Peter

From a.bruselles at gmail.com  Fri Apr  8 08:03:13 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Fri, 8 Apr 2011 14:03:13 +0200
Subject: [EMBOSS] db records retrieve
In-Reply-To: <4D9EEBD4.8020802@ebi.ac.uk>
References: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
	<4D9EEBD4.8020802@ebi.ac.uk>
Message-ID: <BANLkTimBsF43T9x7SPuGaFsVCDvmeOdY1w@mail.gmail.com>

>
> You need to fix or comment out the tsw, emblnew, trembl and nbrf databases
> to avoid those messages. whichdb tries all sequence databases and is a good
> way to catch database that are not working (servers down, data or index
> files not in the expected directory)
>

after commenting those db i get the following:

$: whichdb BCL2L10
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Warning: Cannot open division file '<null>' for database 'em'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'sw'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trhuman'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'human'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'tremblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'swissprot'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'embl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'pir'

   EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed

From dvortsov at img.ras.ru  Wed Apr 13 07:41:52 2011
From: dvortsov at img.ras.ru (Igor Dvortsov)
Date: Wed, 13 Apr 2011 15:41:52 +0400
Subject: [EMBOSS] emboss+cygwin
Message-ID: <4DA58C00.1020703@img.ras.ru>

Hello,
 I'm just trying to install emboss with cygwin on windows 7 and failed.
 latest cygwin release (base,devel packages only) and stable emboss 6.3.1
 complation step normal, seems as everything is built.
 make install - failed, moving all *.dll and *.exe to /usr/local/bin by 
hands
 result - no any response from any program
 b.e., stretcher.exe -help - just terminating without any output.

 so, the question - what to do?

Kind regards, Igor.


From david.bauer at bayer.com  Wed Apr 13 08:03:51 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 13 Apr 2011 14:03:51 +0200
Subject: [EMBOSS] Antwort:  emboss+cygwin
In-Reply-To: <4DA58C00.1020703@img.ras.ru>
Message-ID: <OFD1B38669.8A99333A-ONC1257871.00423397-C1257871.004245DA@bayer.de>

Hi,

did you try the native Windows built mEMBOSS-6.3.1.2-setup.exe on 
ftp://ftp.open-bio.org/pub/EMBOSS/windows/ ?

David.


emboss-bounces at lists.open-bio.org schrieb am 13/04/2011 13:41:52:

> Hello,
>  I'm just trying to install emboss with cygwin on windows 7 and failed.
>  latest cygwin release (base,devel packages only) and stable emboss 
6.3.1
>  complation step normal, seems as everything is built.
>  make install - failed, moving all *.dll and *.exe to /usr/local/bin by 
> hands
>  result - no any response from any program
>  b.e., stretcher.exe -help - just terminating without any output.
> 
>  so, the question - what to do?
> 
> Kind regards, Igor.
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

From fer00000 at yahoo.es  Fri Apr 15 12:43:20 2011
From: fer00000 at yahoo.es (Fernando Negre)
Date: Fri, 15 Apr 2011 17:43:20 +0100 (BST)
Subject: [EMBOSS] Volunteer
Message-ID: <62430.13310.qm@web26906.mail.ukl.yahoo.com>

Hi,

First i introduce myself, I have studied computer science and  i have developed 
in java and in .net in different jobbs for about 5  years (now i am 30 years 
old). I have free hours for each week  and  I am interested in volunteer topics 
about bioinformatics. Mainly I would  like to help in perfonmance topics or 
develop any new functions.
I would like to know any topic to start studing and developing.


Thanks in advance.

From aoife.m.doherty at gmail.com  Fri Apr 22 11:08:17 2011
From: aoife.m.doherty at gmail.com (aoife doherty)
Date: Fri, 22 Apr 2011 16:08:17 +0100
Subject: [EMBOSS] (no subject)
Message-ID: <BANLkTik5_ECu3KOcVwTVFTf5Hymh=7e-nA@mail.gmail.com>

Hi, Am I in the right place to ask a general question about the prophecy
application in EMBOSS? I wanted to use it to build a profile of vertebrate
alignments built with MUSCLE, for use in BLAST. I'm not sure of whether to
use Gribskov/ Henikoff, or whether there is a massive difference in the
results produced between the two?

Thanks
Aoife

From jison at ebi.ac.uk  Mon Apr  4 12:21:42 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Apr 2011 13:21:42 +0100 (BST)
Subject: [EMBOSS] the -orfminsize in SIXPACK and -minsize in GETORF
In-Reply-To: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>
References: <AANLkTin5WfRdcC36QoLCi3namBzucV2b05fphAwD_FjR@mail.gmail.com>
Message-ID: <34843.172.22.100.208.1301919702.squirrel@webmail.ebi.ac.uk>

Hi

Didn't see a reply to you.  Anyhow ...


> Are the options -orfminsize in SIXPACK and -minsize in GETORF the same?

Yes (well, they are equivalent).

> Do they both specify "Minimum nucleotide size of ORF to report"?

Yes - we should probably standardise the names of such options.

> Are these two programs supposed to give the same results under identical
> input parameters?

Without looking at the code I'm not sure.  You might expect slight differences depending on how
exactly an ORF is defined.  They should at least broadly agree.

Cheers

Jon



>
> Thanks
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From jison at ebi.ac.uk  Mon Apr  4 12:25:57 2011
From: jison at ebi.ac.uk (Jon Ison)
Date: Mon, 4 Apr 2011 13:25:57 +0100 (BST)
Subject: [EMBOSS] How to include homing endonucleases?
In-Reply-To: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>
References: <AANLkTimVLvUKG1Y7ncZiCAQ-G5dv0ZavheBjqKBj5xiA@mail.gmail.com>
Message-ID: <58967.172.22.100.208.1301919957.squirrel@webmail.ebi.ac.uk>

Hi Stefanie

Apologies no reply sooner.

You should use rebaseextract
http://emboss.sourceforge.net/apps/cvs/emboss/apps/rebaseextract.html

Details are in the "Data files" section of the "restrict" docs:
http://emboss.sourceforge.net/apps/cvs/emboss/apps/restrict.html

Cheers

Jon




> Hi,
>
> Rebase got a separate file listing all homing  endonuclease
> (ftp://ftp.neb.com/pub/rebase/homing.103), how can I index that file
> as an alternative to rebase? The Emboss  program restrict have the
> option to use a specific datafile, but it's not clear what format that
> file should be?
>
> Regards,
>
> Stefanie Lager
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss
>




From a.bruselles at gmail.com  Thu Apr  7 11:27:35 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Thu, 7 Apr 2011 13:27:35 +0200
Subject: [EMBOSS] databases connection failed
Message-ID: <BANLkTimf8JpR8OC=CSa6Xd7z9gp_xFuntA@mail.gmail.com>

Hi all,
I have a problem with the emboss connection with databases;
this is the output (after a while) when I try whichdb or infoseq:
:~$ whichdb BAC1
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Error: socket connect failed for database 'gba'
socket connect failed for database 'gba': Connection timed out
Warning: Cannot open division file '<null>' for database 'emblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trembl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'nbrf'

  EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed

:~$ infoseq genbank:l07770
Display basic information about sequences
Error: socket connect failed for database 'genbank'
socket connect failed for database 'genbank': Connection timed out
Error: Unable to read sequence 'genbank:l07770'
Died: infoseq terminated: Bad value for '-sequence' and no prompt


Does anyone have an idea of what is happening?

thanks


From a.bruselles at gmail.com  Fri Apr  8 10:27:31 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Fri, 8 Apr 2011 12:27:31 +0200
Subject: [EMBOSS] db records retrieve
Message-ID: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>

Hi all,
I'm not able to retrieve sequences starting from official gene symbols (e.g.
BCL2L10),
what db do I have to use?

This is the output of whichdb:

*$ whichdb BCL2L10 -debug
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Warning: Cannot open division file '<null>' for database 'tsw'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'emblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trembl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'nbrf'

   EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed*

Thanks


From pmr at ebi.ac.uk  Fri Apr  8 11:04:52 2011
From: pmr at ebi.ac.uk (Peter Rice)
Date: Fri, 08 Apr 2011 12:04:52 +0100
Subject: [EMBOSS] db records retrieve
In-Reply-To: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
References: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
Message-ID: <4D9EEBD4.8020802@ebi.ac.uk>

On 08/04/2011 11:27, Alessandro Bruselles wrote:
> Hi all,
> I'm not able to retrieve sequences starting from official gene symbols (e.g.
> BCL2L10),
> what db do I have to use?

You need a database you can search by gene name. If the database has 
access through a website you can use the URL access method ... providing 
a URL that returns with the sequence in a format that EMBOSS can read.

For UniProt:

DB uniprotgene [
   type: "protein"
   format: "swiss"
   methodquery: "url"
   url: 
"http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-gen:%s]+-ascii"
]

(the URL should be all in one line)

We will have other ways to do this in EMBOSS 6.4.0 when we enable gen 
and other database search fields.

> This is the output of whichdb:
>
> *$ whichdb BCL2L10 -debug
> Search all sequence databases for an entry and retrieve it
> Output file [outfile.whichdb]: stdout
> Warning: Cannot open division file '<null>' for database 'tsw'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'emblnew'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'trembl'
> Warning: seqCdQry failed
> Warning: Cannot open division file '<null>' for database 'nbrf'
>
>     EMBOSS An error in ajseqdb.c at line 5350:
> seqCdQryOpen failed*

You need to fix or comment out the tsw, emblnew, trembl and nbrf 
databases to avoid those messages. whichdb tries all sequence databases 
and is a good way to catch database that are not working (servers down, 
data or index files not in the expected directory)

Hope this helps

Peter


From a.bruselles at gmail.com  Fri Apr  8 12:03:13 2011
From: a.bruselles at gmail.com (Alessandro Bruselles)
Date: Fri, 8 Apr 2011 14:03:13 +0200
Subject: [EMBOSS] db records retrieve
In-Reply-To: <4D9EEBD4.8020802@ebi.ac.uk>
References: <BANLkTin5rEC-vGXs=xp-Ncn0aBFW_-F=kQ@mail.gmail.com>
	<4D9EEBD4.8020802@ebi.ac.uk>
Message-ID: <BANLkTimBsF43T9x7SPuGaFsVCDvmeOdY1w@mail.gmail.com>

>
> You need to fix or comment out the tsw, emblnew, trembl and nbrf databases
> to avoid those messages. whichdb tries all sequence databases and is a good
> way to catch database that are not working (servers down, data or index
> files not in the expected directory)
>

after commenting those db i get the following:

$: whichdb BCL2L10
Search all sequence databases for an entry and retrieve it
Output file [outfile.whichdb]: stdout
Warning: Cannot open division file '<null>' for database 'em'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'sw'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'trhuman'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'human'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'tremblnew'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'swissprot'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'embl'
Warning: seqCdQry failed
Warning: Cannot open division file '<null>' for database 'pir'

   EMBOSS An error in ajseqdb.c at line 5350:
seqCdQryOpen failed


From dvortsov at img.ras.ru  Wed Apr 13 11:41:52 2011
From: dvortsov at img.ras.ru (Igor Dvortsov)
Date: Wed, 13 Apr 2011 15:41:52 +0400
Subject: [EMBOSS] emboss+cygwin
Message-ID: <4DA58C00.1020703@img.ras.ru>

Hello,
 I'm just trying to install emboss with cygwin on windows 7 and failed.
 latest cygwin release (base,devel packages only) and stable emboss 6.3.1
 complation step normal, seems as everything is built.
 make install - failed, moving all *.dll and *.exe to /usr/local/bin by 
hands
 result - no any response from any program
 b.e., stretcher.exe -help - just terminating without any output.

 so, the question - what to do?

Kind regards, Igor.



From david.bauer at bayer.com  Wed Apr 13 12:03:51 2011
From: david.bauer at bayer.com (david.bauer at bayer.com)
Date: Wed, 13 Apr 2011 14:03:51 +0200
Subject: [EMBOSS] Antwort:  emboss+cygwin
In-Reply-To: <4DA58C00.1020703@img.ras.ru>
Message-ID: <OFD1B38669.8A99333A-ONC1257871.00423397-C1257871.004245DA@bayer.de>

Hi,

did you try the native Windows built mEMBOSS-6.3.1.2-setup.exe on 
ftp://ftp.open-bio.org/pub/EMBOSS/windows/ ?

David.


emboss-bounces at lists.open-bio.org schrieb am 13/04/2011 13:41:52:

> Hello,
>  I'm just trying to install emboss with cygwin on windows 7 and failed.
>  latest cygwin release (base,devel packages only) and stable emboss 
6.3.1
>  complation step normal, seems as everything is built.
>  make install - failed, moving all *.dll and *.exe to /usr/local/bin by 
> hands
>  result - no any response from any program
>  b.e., stretcher.exe -help - just terminating without any output.
> 
>  so, the question - what to do?
> 
> Kind regards, Igor.
> 
> _______________________________________________
> EMBOSS mailing list
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss


From fer00000 at yahoo.es  Fri Apr 15 16:43:20 2011
From: fer00000 at yahoo.es (Fernando Negre)
Date: Fri, 15 Apr 2011 17:43:20 +0100 (BST)
Subject: [EMBOSS] Volunteer
Message-ID: <62430.13310.qm@web26906.mail.ukl.yahoo.com>

Hi,

First i introduce myself, I have studied computer science and  i have developed 
in java and in .net in different jobbs for about 5  years (now i am 30 years 
old). I have free hours for each week  and  I am interested in volunteer topics 
about bioinformatics. Mainly I would  like to help in perfonmance topics or 
develop any new functions.
I would like to know any topic to start studing and developing.


Thanks in advance.


From aoife.m.doherty at gmail.com  Fri Apr 22 15:08:17 2011
From: aoife.m.doherty at gmail.com (aoife doherty)
Date: Fri, 22 Apr 2011 16:08:17 +0100
Subject: [EMBOSS] (no subject)
Message-ID: <BANLkTik5_ECu3KOcVwTVFTf5Hymh=7e-nA@mail.gmail.com>

Hi, Am I in the right place to ask a general question about the prophecy
application in EMBOSS? I wanted to use it to build a profile of vertebrate
alignments built with MUSCLE, for use in BLAST. I'm not sure of whether to
use Gribskov/ Henikoff, or whether there is a massive difference in the
results produced between the two?

Thanks
Aoife