From mad at biol.unlp.edu.ar  Mon Aug  9 09:00:30 2004
From: mad at biol.unlp.edu.ar (Martin Sarachu)
Date: Mon,  9 Aug 2004 10:00:30 -0300
Subject: [EMBOSS] EMBOSS wrappers - Beta release
Message-ID: <1092056430.4117756ec4b7c@nahuel.biol.unlp.edu.ar>

Dear EMBOSSers,

this is to announce BETA release of the EMBOSS wrappers. These wrappers
add a number of programs to your EMBOSS distribution, being:

Programs in CLUSTAL wrapper
* clustal: Global multiple alignment of sequences
* clustalnj: Neighbor-Joining phylogenetic tree from multiple alignment

Programs in BLAST wrapper
* blast: BLAST search of query sequence(s) against sequence search set
* blast2seq: Finds local alignments between two sequences, using BLAST
* phiblast: Search protein sequence set combining matching of pattern
with local alignment of a query sequence surrounding the match
* psiblast: Iterative BLAST search with generation of profile of protein
sequence against protein sequence set
* makeblastdb: Make BLAST format sequence database using formatdb

Programs in fastA wrapper
* fastasearch: fastA search of query sequence(s) against sequence search set
* fasta2seq: Finds local alignments between two sequences, using fastA
* fastapid: Protein identification from peptides using fastA algorithm

Programs in ps_scan & pf_make wrapper
* ps_scan: Scans proteins against patterns, profiles and rules of PROSITE
* pf_make: Creates PROSITE style profile from protein multiple alignment

Programs in bscan wrapper
* bscan: Scans proteins or nucleic acids using Blocks

All the wrappers are the work of Guy Bottu <gbottu at ben.vub.ac.be> and
this installation script is the work of Martin Sarachu
<msarachu at biol.unlp.edu.ar>.
This is a joint effort between the Belgian and Argentinian EMBnet nodes.

This release is fully compatible with EMBOSS-2.8.0 and partially
compatible with EMBOSS-2.9.0 (only bscan, ps_scan & pf_make wrappers), a
new release is being prepared for EMBOSS-2.9.0

You can download the wrappers from the wEMBOSS site, here
http://www.wemboss.org/Folder.2003-09-11.4050/Folder.2003-09-11.2502/wrappers4EMBOSS-0.1b.tar.gz

Please place all your questions & comments on the wrappers4EMBOSS Forums at
http://www.wemboss.org

The wrappers has been succesfully tested on Linux RedHat 9.


Regards,

Martin

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


From mikeyueli at hotmail.com  Mon Aug  9 09:46:42 2004
From: mikeyueli at hotmail.com (Li Yue)
Date: Mon, 9 Aug 2004 21:46:42 +0800
Subject: [EMBOSS] Asking for help
Message-ID: <BAY1-DAV4WmQusPWMhi00005d53@hotmail.com>

Dear Sir or Madam??

	     I am a rookie who is learning how to use the emboss.And I find 
a problem always haunting me.Whenever I run a program which uses a database 
entry as the input,such as the "stretcher","needle","matcher" and so on,
a problem occurs.For example,when I input "tsw:hba_human" as an input sequence of
the "stretcher",the following prompt message is displayed:


       warning:cannot open division file '<null>' for database 'tsw'
       warning:seqCdQry failed 
       Error: Unable to read sequence 'tsw:hba_human' 

When I run other programs which used another test database "tembl",the same problem also occurs:

       warning:cannot open division file '<null>' for database 'tembl'
       warning:seqCdQry failed 
       Error: Unable to read sequence 'tembl:ap000504' 
????????????????

         I really follow the instructions in your web site strictly to set up the 
emboss.default file and the status of those database could be proved correct by invoking "showdb".
The current version of the emboss in my computer is 2.9.0. Could you please tell me how to 
solve this problem?



         Thank you very much for your great help.Best wishes to you! 


	

????????????????
 				

????????????????Mike Li 
????????????????mikeyueli at hotmail.com
????????????????????2004-08-09

From Caroline.Barretto at rdls.nestle.com  Mon Aug  9 09:54:10 2004
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Mon, 9 Aug 2004 15:54:10 +0200
Subject: [EMBOSS] eprimer3
Message-ID: <79B17B88C9A807458D4EA5A03061BB51042132@chlsne00.nestle.com>

Hello,

Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.

Many thanks,

Caroline.


From gwilliam at hgmp.mrc.ac.uk  Mon Aug  9 10:26:58 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Mon, 09 Aug 2004 15:26:58 +0100
Subject: [EMBOSS] eprimer3
References: <79B17B88C9A807458D4EA5A03061BB51042132@chlsne00.nestle.com>
Message-ID: <411789B2.B818C7D0@hgmp.mrc.ac.uk>

Caroline,

I've just tried this with 4.7 Mb of E. coli genome with no problems.

Regards,
Gary

"Barretto,Caroline,LAUSANNE,NRC/BAS" wrote:
> 
> Hello,
> 
> Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.
> 
> Many thanks,
> 
> Caroline.

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


From Caroline.Barretto at rdls.nestle.com  Mon Aug  9 06:22:35 2004
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Mon, 9 Aug 2004 10:22:35 -0000
Subject: [EMBOSS] eprimer3
Message-ID: <79B17B88C9A807458D4EA5A03061BB51064409@chlsne00.nestle.com>

Hello,

Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.

Many thanks,

Caroline.
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From David.Bauer at SCHERING.DE  Tue Aug 10 02:55:00 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Tue, 10 Aug 2004 08:55:00 +0200
Subject: Antwort: [EMBOSS] eprimer3
Message-ID: <OF5E9F19AA.FCC0A830-ONC1256EEC.001DE6BE-C1256EEC.0025FEE1@schering.de>


Hi Caroline,

there seems to be a problem that may be architecture and/or memory
dependent.

I did a test with a 2.3 Mb sequence and got an totally empty output list.
So I tested a bit with different sequence length:
It works OK up to:
-numreturn 10 -pickanyway -sbegin 1 -send 2100000
But I get an empty output with:
-numreturn 10 -pickanyway -sbegin 1 -send 2200000
And the output is OK again with
-numreturn 10 -pickanyway -sbegin 100000 -send 2200000

The system is FreeBSD on Intel with 768 Mb RAM.

Here is the debug ouput in case I get an empty output list:
The negative numbers for memory use do not look really healthy to me :-(
Final Summary
=============
String usage (bytes): -1556553655 allocated, 17 freed, -1554743706 in use
String usage (number): 160768 allocated, 0 freed 159728 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): -1553262663 allocated, 17 reallocated 8390208 zeroed
Memory usage (number): 368042 allocates, 0 frees, 365811 resizes, 0 in use


In case the output was OK the memory allocation looks much better and is
very close to what I have available as physical RAM.
Final Summary
=============
String usage (bytes): 711486205 allocated, 16 freed, 713296154 in use
String usage (number): 158674 allocated, 0 freed 157634 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): 714748493 allocated, 16 reallocated 8390208 zeroed
Memory usage (number): 364254 allocates, 0 frees, 362023 resizes, 0 in use

Gary, I hope you have an idea how to fix this ;-)

Cheers,
David.



                                                                                                                    
                      "Barretto,Caroline,LAUSAN                                                                     
                      NE,NRC/BAS"                                                                                   
                      <Caroline.Barretto at rdls.n         An:      <emboss at hgmp.mrc.ac.uk>                            
                      estle.com>                        Kopie:                                                      
                      Gesendet von:                     Thema:   [EMBOSS] eprimer3                                  
                      owner-emboss at hgmp.mrc.ac.                                                                     
                      uk                                                                                            
                                                                                                                    
                                                                                                                    
                      09.08.2004 12:22                                                                              
                                                                                                                    
                                                                                                                    




Hello,


Is it possible to use eprimer3 on a complete bacterial genome or do we have
to give a smaller sequence? I have tried with a genome of 2,3Mbases but I
never get any result.


Many thanks,


Caroline.










From kellert at ohsu.edu  Wed Aug 11 19:41:07 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Wed, 11 Aug 2004 16:41:07 -0700
Subject: [EMBOSS] annotation
Message-ID: <EAF91470-EBEF-11D8-90DB-0003930405E2@ohsu.edu>

Greetings,
Could someone recommend an efficient way to get the annotation for the 
best hits from a blast search?
In other words, if I run megablast and get back a list of matches with 
a cutoff e-value, what's a good way to get to get the gene name (if 
known) for the hit?

Thanks,
Tom Keller

Thomas J. Keller, Ph.D.
Director, MMI Core Facility
Oregon Health & Science University
3181 SW Sam Jackson Park Rd.
Portland, OR, USA,   97239

http://www.ohsu.edu/research/core
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From gwilliam at hgmp.mrc.ac.uk  Thu Aug 12 05:01:46 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Thu, 12 Aug 2004 10:01:46 +0100
Subject: [EMBOSS] annotation
References: <EAF91470-EBEF-11D8-90DB-0003930405E2@ohsu.edu>
Message-ID: <411B31FA.46B67620@hgmp.mrc.ac.uk>

Tom,

If you can change your list of matching IDs to a list of EMBOSS USAs,
then maybe somthing like the following might do what you require:


showfeat @list-of-your-ids -matchtag gene -values -pos -tag -stricttag
-width 0 -nodescription -noid -notype -out oputfile -auto

For example:
showfeat em:hsfau -matchtag gene -values -pos -tag -stricttag -width 0
-nodescription -noid -notype -auto stdout

57-458  gene="fau" 

Regards,
Gary


Thomas J Keller wrote:
> 
> Greetings,
> Could someone recommend an efficient way to get the annotation for the best hits from a blast search?
> In other words, if I run megablast and get back a list of matches with a cutoff e-value, what's a good way to get to get the gene name (if known) for the hit?
> 
> Thanks,
> Tom Keller
> 
> Thomas J. Keller, Ph.D.
> Director, MMI Core Facility
> Oregon Health & Science University
> 3181 SW Sam Jackson Park Rd.
> Portland, OR, USA, 97239
> 
> http://www.ohsu.edu/research/core

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


From bioinfovijayaraj at yahoo.com  Mon Aug 16 05:07:20 2004
From: bioinfovijayaraj at yahoo.com (vijayaraj nagarajan)
Date: Mon, 16 Aug 2004 02:07:20 -0700 (PDT)
Subject: [EMBOSS] showdb-not-listing
Message-ID: <20040816090720.2170.qmail@web90104.mail.scd.yahoo.com>

hi friends
i am a newbie..just installed emboss.
my showdb command...doesnt list any databases...
whats the problem..
pls help.

Thanks in advance
vijay


		
__________________________________
Do you Yahoo!?
Yahoo! Mail - 50x more storage than other providers!
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From sbassi at gmail.com  Fri Aug 20 16:45:51 2004
From: sbassi at gmail.com (Sebastian Bassi)
Date: Fri, 20 Aug 2004 17:45:51 -0300
Subject: [EMBOSS] Compiling options
Message-ID: <b43bf20804082013455b0fb0f6@mail.gmail.com>

Hello,

I'd like to know if the the X lib path you pass as a compiling option,
are used at compile time or at run time.
The answer to this question will be used to include EMBOSS in DNALinux
with graphical support. EMBOSS 2.8.0 is already included in DNALinux,
but without graphical support.
Since is a liveCD, the compiling enviroment is different from the
enviroment that it runs.
So the question is: Wich X path should I pass when compiling? The
compiling system path or the running path?

Here are the path I am talking about:

To get X-windows based output you must have X installed, or else
PLplot will not build the required driver. You may need to specify the
location of your X-windows library with the configuration options:
-x-includes=DIR (X include files are in DIR) -x-libraries=DIR (X
library files are in DIR)



From mad at biol.unlp.edu.ar  Mon Aug  9 13:00:30 2004
From: mad at biol.unlp.edu.ar (Martin Sarachu)
Date: Mon,  9 Aug 2004 10:00:30 -0300
Subject: [EMBOSS] EMBOSS wrappers - Beta release
Message-ID: <1092056430.4117756ec4b7c@nahuel.biol.unlp.edu.ar>

Dear EMBOSSers,

this is to announce BETA release of the EMBOSS wrappers. These wrappers
add a number of programs to your EMBOSS distribution, being:

Programs in CLUSTAL wrapper
* clustal: Global multiple alignment of sequences
* clustalnj: Neighbor-Joining phylogenetic tree from multiple alignment

Programs in BLAST wrapper
* blast: BLAST search of query sequence(s) against sequence search set
* blast2seq: Finds local alignments between two sequences, using BLAST
* phiblast: Search protein sequence set combining matching of pattern
with local alignment of a query sequence surrounding the match
* psiblast: Iterative BLAST search with generation of profile of protein
sequence against protein sequence set
* makeblastdb: Make BLAST format sequence database using formatdb

Programs in fastA wrapper
* fastasearch: fastA search of query sequence(s) against sequence search set
* fasta2seq: Finds local alignments between two sequences, using fastA
* fastapid: Protein identification from peptides using fastA algorithm

Programs in ps_scan & pf_make wrapper
* ps_scan: Scans proteins against patterns, profiles and rules of PROSITE
* pf_make: Creates PROSITE style profile from protein multiple alignment

Programs in bscan wrapper
* bscan: Scans proteins or nucleic acids using Blocks

All the wrappers are the work of Guy Bottu <gbottu at ben.vub.ac.be> and
this installation script is the work of Martin Sarachu
<msarachu at biol.unlp.edu.ar>.
This is a joint effort between the Belgian and Argentinian EMBnet nodes.

This release is fully compatible with EMBOSS-2.8.0 and partially
compatible with EMBOSS-2.9.0 (only bscan, ps_scan & pf_make wrappers), a
new release is being prepared for EMBOSS-2.9.0

You can download the wrappers from the wEMBOSS site, here
http://www.wemboss.org/Folder.2003-09-11.4050/Folder.2003-09-11.2502/wrappers4EMBOSS-0.1b.tar.gz

Please place all your questions & comments on the wrappers4EMBOSS Forums at
http://www.wemboss.org

The wrappers has been succesfully tested on Linux RedHat 9.


Regards,

Martin

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


From mikeyueli at hotmail.com  Mon Aug  9 13:46:42 2004
From: mikeyueli at hotmail.com (Li Yue)
Date: Mon, 9 Aug 2004 21:46:42 +0800
Subject: [EMBOSS] Asking for help
Message-ID: <BAY1-DAV4WmQusPWMhi00005d53@hotmail.com>

Dear Sir or Madam?

	     I am a rookie who is learning how to use the emboss.And I find 
a problem always haunting me.Whenever I run a program which uses a database 
entry as the input,such as the "stretcher","needle","matcher" and so on,
a problem occurs.For example,when I input "tsw:hba_human" as an input sequence of
the "stretcher",the following prompt message is displayed:


       warning:cannot open division file '<null>' for database 'tsw'
       warning:seqCdQry failed 
       Error: Unable to read sequence 'tsw:hba_human' 

When I run other programs which used another test database "tembl",the same problem also occurs:

       warning:cannot open division file '<null>' for database 'tembl'
       warning:seqCdQry failed 
       Error: Unable to read sequence 'tembl:ap000504' 
????????

         I really follow the instructions in your web site strictly to set up the 
emboss.default file and the status of those database could be proved correct by invoking "showdb".
The current version of the emboss in my computer is 2.9.0. Could you please tell me how to 
solve this problem?



         Thank you very much for your great help.Best wishes to you! 


	

????????
 				

????????Mike Li 
????????mikeyueli at hotmail.com
??????????2004-08-09

From Caroline.Barretto at rdls.nestle.com  Mon Aug  9 13:54:10 2004
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Mon, 9 Aug 2004 15:54:10 +0200
Subject: [EMBOSS] eprimer3
Message-ID: <79B17B88C9A807458D4EA5A03061BB51042132@chlsne00.nestle.com>

Hello,

Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.

Many thanks,

Caroline.


From gwilliam at hgmp.mrc.ac.uk  Mon Aug  9 14:26:58 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Mon, 09 Aug 2004 15:26:58 +0100
Subject: [EMBOSS] eprimer3
References: <79B17B88C9A807458D4EA5A03061BB51042132@chlsne00.nestle.com>
Message-ID: <411789B2.B818C7D0@hgmp.mrc.ac.uk>

Caroline,

I've just tried this with 4.7 Mb of E. coli genome with no problems.

Regards,
Gary

"Barretto,Caroline,LAUSANNE,NRC/BAS" wrote:
> 
> Hello,
> 
> Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.
> 
> Many thanks,
> 
> Caroline.

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


From Caroline.Barretto at rdls.nestle.com  Mon Aug  9 10:22:35 2004
From: Caroline.Barretto at rdls.nestle.com (Barretto,Caroline,LAUSANNE,NRC/BAS)
Date: Mon, 9 Aug 2004 10:22:35 -0000
Subject: [EMBOSS] eprimer3
Message-ID: <79B17B88C9A807458D4EA5A03061BB51064409@chlsne00.nestle.com>

Hello,

Is it possible to use eprimer3 on a complete bacterial genome or do we have to give a smaller sequence? I have tried with a genome of 2,3Mbases but I never get any result.

Many thanks,

Caroline.
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From David.Bauer at SCHERING.DE  Tue Aug 10 06:55:00 2004
From: David.Bauer at SCHERING.DE (David.Bauer at SCHERING.DE)
Date: Tue, 10 Aug 2004 08:55:00 +0200
Subject: Antwort: [EMBOSS] eprimer3
Message-ID: <OF5E9F19AA.FCC0A830-ONC1256EEC.001DE6BE-C1256EEC.0025FEE1@schering.de>


Hi Caroline,

there seems to be a problem that may be architecture and/or memory
dependent.

I did a test with a 2.3 Mb sequence and got an totally empty output list.
So I tested a bit with different sequence length:
It works OK up to:
-numreturn 10 -pickanyway -sbegin 1 -send 2100000
But I get an empty output with:
-numreturn 10 -pickanyway -sbegin 1 -send 2200000
And the output is OK again with
-numreturn 10 -pickanyway -sbegin 100000 -send 2200000

The system is FreeBSD on Intel with 768 Mb RAM.

Here is the debug ouput in case I get an empty output list:
The negative numbers for memory use do not look really healthy to me :-(
Final Summary
=============
String usage (bytes): -1556553655 allocated, 17 freed, -1554743706 in use
String usage (number): 160768 allocated, 0 freed 159728 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): -1553262663 allocated, 17 reallocated 8390208 zeroed
Memory usage (number): 368042 allocates, 0 frees, 365811 resizes, 0 in use


In case the output was OK the memory allocation looks much better and is
very close to what I have available as physical RAM.
Final Summary
=============
String usage (bytes): 711486205 allocated, 16 freed, 713296154 in use
String usage (number): 158674 allocated, 0 freed 157634 in use
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
Table usage : 3 opened, 0 closed, 251 maxsize, 24 maxmem
List usage : 11 opened, 8 closed, 0 maxsize 5970 nodes
List iterator usage : 11 opened, 11 closed, 0 maxsize
Regexp usage (bytes): 112 allocated, 0 freed, 0 in use
Regexp usage (number): 28 allocated, 0 freed 0 in use
File usage : 1 opened, 5 closed, 3 max, 6 total
ajNamExit done
Memory usage (bytes): 714748493 allocated, 16 reallocated 8390208 zeroed
Memory usage (number): 364254 allocates, 0 frees, 362023 resizes, 0 in use

Gary, I hope you have an idea how to fix this ;-)

Cheers,
David.



                                                                                                                    
                      "Barretto,Caroline,LAUSAN                                                                     
                      NE,NRC/BAS"                                                                                   
                      <Caroline.Barretto at rdls.n         An:      <emboss at hgmp.mrc.ac.uk>                            
                      estle.com>                        Kopie:                                                      
                      Gesendet von:                     Thema:   [EMBOSS] eprimer3                                  
                      owner-emboss at hgmp.mrc.ac.                                                                     
                      uk                                                                                            
                                                                                                                    
                                                                                                                    
                      09.08.2004 12:22                                                                              
                                                                                                                    
                                                                                                                    




Hello,


Is it possible to use eprimer3 on a complete bacterial genome or do we have
to give a smaller sequence? I have tried with a genome of 2,3Mbases but I
never get any result.


Many thanks,


Caroline.










From kellert at ohsu.edu  Wed Aug 11 23:41:07 2004
From: kellert at ohsu.edu (Thomas J Keller)
Date: Wed, 11 Aug 2004 16:41:07 -0700
Subject: [EMBOSS] annotation
Message-ID: <EAF91470-EBEF-11D8-90DB-0003930405E2@ohsu.edu>

Greetings,
Could someone recommend an efficient way to get the annotation for the 
best hits from a blast search?
In other words, if I run megablast and get back a list of matches with 
a cutoff e-value, what's a good way to get to get the gene name (if 
known) for the hit?

Thanks,
Tom Keller

Thomas J. Keller, Ph.D.
Director, MMI Core Facility
Oregon Health & Science University
3181 SW Sam Jackson Park Rd.
Portland, OR, USA,   97239

http://www.ohsu.edu/research/core
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From gwilliam at hgmp.mrc.ac.uk  Thu Aug 12 09:01:46 2004
From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522)
Date: Thu, 12 Aug 2004 10:01:46 +0100
Subject: [EMBOSS] annotation
References: <EAF91470-EBEF-11D8-90DB-0003930405E2@ohsu.edu>
Message-ID: <411B31FA.46B67620@hgmp.mrc.ac.uk>

Tom,

If you can change your list of matching IDs to a list of EMBOSS USAs,
then maybe somthing like the following might do what you require:


showfeat @list-of-your-ids -matchtag gene -values -pos -tag -stricttag
-width 0 -nodescription -noid -notype -out oputfile -auto

For example:
showfeat em:hsfau -matchtag gene -values -pos -tag -stricttag -width 0
-nodescription -noid -notype -auto stdout

57-458  gene="fau" 

Regards,
Gary


Thomas J Keller wrote:
> 
> Greetings,
> Could someone recommend an efficient way to get the annotation for the best hits from a blast search?
> In other words, if I run megablast and get back a list of matches with a cutoff e-value, what's a good way to get to get the gene name (if known) for the hit?
> 
> Thanks,
> Tom Keller
> 
> Thomas J. Keller, Ph.D.
> Director, MMI Core Facility
> Oregon Health & Science University
> 3181 SW Sam Jackson Park Rd.
> Portland, OR, USA, 97239
> 
> http://www.ohsu.edu/research/core

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


From bioinfovijayaraj at yahoo.com  Mon Aug 16 09:07:20 2004
From: bioinfovijayaraj at yahoo.com (vijayaraj nagarajan)
Date: Mon, 16 Aug 2004 02:07:20 -0700 (PDT)
Subject: [EMBOSS] showdb-not-listing
Message-ID: <20040816090720.2170.qmail@web90104.mail.scd.yahoo.com>

hi friends
i am a newbie..just installed emboss.
my showdb command...doesnt list any databases...
whats the problem..
pls help.

Thanks in advance
vijay


		
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From sbassi at gmail.com  Fri Aug 20 20:45:51 2004
From: sbassi at gmail.com (Sebastian Bassi)
Date: Fri, 20 Aug 2004 17:45:51 -0300
Subject: [EMBOSS] Compiling options
Message-ID: <b43bf20804082013455b0fb0f6@mail.gmail.com>

Hello,

I'd like to know if the the X lib path you pass as a compiling option,
are used at compile time or at run time.
The answer to this question will be used to include EMBOSS in DNALinux
with graphical support. EMBOSS 2.8.0 is already included in DNALinux,
but without graphical support.
Since is a liveCD, the compiling enviroment is different from the
enviroment that it runs.
So the question is: Wich X path should I pass when compiling? The
compiling system path or the running path?

Here are the path I am talking about:

To get X-windows based output you must have X installed, or else
PLplot will not build the required driver. You may need to specify the
location of your X-windows library with the configuration options:
-x-includes=DIR (X include files are in DIR) -x-libraries=DIR (X
library files are in DIR)