[BiO BB] RE:

[Venkata Satagopam]

Yes, you can get the full entry of GenBank 
from any public SRS servers. Here is the 
link where you can found many public SRS
servers..
http://www.lionbio.co.uk/publicsrs.html

OR you can look at http://igbmc.u-strasbg.fr/srs6/

regards
venkata

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Posted At: Tuesday, January 01, 1991 1:00 AM
Posted To: Inbox
Conversation: 
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Today's Topics:

   1. Re: Is it possible to Blast against genBank files (jordan swanson)
   2. Re: Is it possible to Blast against genBank files (Iddo Friedberg)
   3. Re: Is it possible to Blast against genBank files (Boris Steipe)

--__--__--

Message: 1
Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST)
From: jordan swanson <jordanmswanson at yahoo.com>
Subject: Re: [BiO BB] Is it possible to Blast against genBank files
To: bio_bulletin_board at bioinformatics.org
Reply-To: bio_bulletin_board at bioinformatics.org

> You mean that the BLAST results only have the Fasta
> file annotation in 
> them. Well, AFAIK, the only input to formatdb is
> Fasta or ASN.1. The 
> output, anyhow, would be a one-liner.
> 
> How about giving her the output in HTML (-T option)?
> blast automatically 
> builds a link from each hit to the NCBI page. So
> using a browser, your 
> coworker can skim the one-line annotation, and then
> click & delve into 
> the more interesting ones.

We did try that, however with the large number of
sequences she needed to look up, she was black-listed
from their machine.  We need to find the full GenBank
entry given a particular identifier, unfortunately the
easiest way I've found so far seems to be the Entrez
system, and that appears to not be possible to
download.  Is there another way to get the full
genbank entry given the identifier?

---
Jordan Swanson

__________________________________
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--__--__--

Message: 2
Date: Thu, 18 Dec 2003 13:00:25 -0800
From: Iddo Friedberg <idoerg at burnham.org>
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] Is it possible to Blast against genBank files
Reply-To: bio_bulletin_board at bioinformatics.org

Biopython has something that can do that. Maybe Bioperl too. Let me know 
if you want the Python code.

./I

jordan swanson wrote:
>>You mean that the BLAST results only have the Fasta
>>file annotation in 
>>them. Well, AFAIK, the only input to formatdb is
>>Fasta or ASN.1. The 
>>output, anyhow, would be a one-liner.
>>
>>How about giving her the output in HTML (-T option)?
>>blast automatically 
>>builds a link from each hit to the NCBI page. So
>>using a browser, your 
>>coworker can skim the one-line annotation, and then
>>click & delve into 
>>the more interesting ones.
> 
> 
> We did try that, however with the large number of
> sequences she needed to look up, she was black-listed
> from their machine.  We need to find the full GenBank
> entry given a particular identifier, unfortunately the
> easiest way I've found so far seems to be the Entrez
> system, and that appears to not be possible to
> download.  Is there another way to get the full
> genbank entry given the identifier?
> 
> ---
> Jordan Swanson
> 
> __________________________________
> Do you Yahoo!?
> New Yahoo! Photos - easier uploading and sharing.
> http://photos.yahoo.com/
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo


--__--__--

Message: 3
Date: Thu, 18 Dec 2003 17:01:20 -0500
From: Boris Steipe <boris.steipe at utoronto.ca>
To: bio_bulletin_board at bioinformatics.org
Subject: Re: [BiO BB] Is it possible to Blast against genBank files
Reply-To: bio_bulletin_board at bioinformatics.org

jordan swanson wrote:
> 
> > You mean that the BLAST results only have the Fasta
> > file annotation in
> > them. Well, AFAIK, the only input to formatdb is
> > Fasta or ASN.1. The
> > output, anyhow, would be a one-liner.
> >
> > How about giving her the output in HTML (-T option)?
> > blast automatically
> > builds a link from each hit to the NCBI page. So
> > using a browser, your
> > coworker can skim the one-line annotation, and then
> > click & delve into
> > the more interesting ones.
> 
> We did try that, however with the large number of
> sequences she needed to look up, she was black-listed
> from their machine.  We need to find the full GenBank
> entry given a particular identifier, unfortunately the
> easiest way I've found so far seems to be the Entrez
> system, and that appears to not be possible to
> download.  Is there another way to get the full
> genbank entry given the identifier?
> 
> ---
> Jordan Swanson

Yes, you can get the files through the SeqHound remote Perl API - easy to
program and no blacklists.

See:            <http://blueprint.org/seqhound/seqhound.html>
and especially: <http://blueprint.org/seqhound/api_help/apifunctslist.html>


Best regards,


Boris

---
Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics
http://biochemistry.utoronto.ca/steipe


--__--__--

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End of BiO_Bulletin_Board Digest
=====
Venkata Pardhasaradhi Satagopam, 
Bioinformatics Scientist, 
Genomics IT Research, 
Office Address  :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414
Home Address    :Fritz-Frey-Str.8/112.301.01, 
69121 HEIDELBERG, GERMANY. Tel:0049-(0)6221 729667
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