[Bioperl-l] Refseq Version
Mark A. Jensen
maj at fortinbras.us
Fri Feb 5 10:03:49 EST 2010
Hey guys-- thanks for this conversation, pls resist the temptation to go offlist
When Russell provides the info, we can possibly add a new accesor for the
----- Original Message -----
From: "shalu sharma" <sharmashalu.bio at gmail.com>
To: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 9:55 AM
Subject: Re: [Bioperl-l] Refseq Version
> Hi Russell,
> Thanks for your response.
> I am getting the number of sequence in the database but not the release
> number (like 38, 39).
> This is what i did:
> $ fastacmd -I -d /db/ncbiblast/refseq/refseq_protein
> Database: NCBI Protein Reference Sequences
> 7,585,993 sequences; 2,644,770,521 total letters
> File names:
> Date: Jan 30, 2010 8:34 PM Version: 4 Longest sequence: 36,805 res
> Date: Jan 30, 2010 8:34 PM Version: 4 Longest sequence: 33,403 res
> Date: Jan 30, 2010 8:34 PM Version: 4 Longest sequence: 15,830 res
> I am still confuse that how i can get the release number. I know refseq 39
> was released on Jan 30, 2010 but i don't know how to confirm this. I also
> tried look refseq release file but was not able to get any thing.
> I would really appreciate if anyone can help me out with this.
> On Thu, Feb 4, 2010 at 6:39 PM, Smithies, Russell <
> Russell.Smithies at agresearch.co.nz> wrote:
>> If you have access to the blast database, use fastacmd -I -d databasename
>> Otherwise, it's usually at the bottom of your blast result.
>> > -----Original Message-----
>> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> > bounces at lists.open-bio.org] On Behalf Of shalu sharma
>> > Sent: Friday, 5 February 2010 11:02 a.m.
>> > To: bioperl-l at lists.open-bio.org
>> > Subject: [Bioperl-l] Refseq Version
>> > Hi All,
>> > This is not a bioperl query.
>> > Is there any way to check refseq version (release). Actually i am using
>> > some
>> > server to blast my sequences (blastall) against refseq. Is there any way
>> > can get the version information on the refseq database (from the blast
>> > file
>> > or directly from the database)?
>> > Thanks
>> > Shalu
>> > _______________________________________________
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