Smithies, Russell | 24 Apr 00:32 2013
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Re: Taxa Id from blast report

It works OK if I do it with NCBI's pre-formatted databases, eg.

illustrious$ blastx -query gold_small.fa -db /bifo/infernal/active/blastdata/mirror/nr 
-max_target_seqs 1 -outfmt "6 staxids sscinames sskingdoms"
411903  Collinsella aerofaciens ATCC 25986      Bacteria
411903  Collinsella aerofaciens ATCC 25986      Bacteria
39947   Oryza sativa Japonica Group     Eukaryota
39947   Oryza sativa Japonica Group     Eukaryota
39947   Oryza sativa Japonica Group     Eukaryota
498761  Heliobacterium modesticaldum Ice1       Bacteria
391296  Streptococcus suis 98HAH33      Bacteria
391296  Streptococcus suis 98HAH33      Bacteria

Perhaps it's something to do with your database formatting or sequence IDs?

--Russell

From: shalu sharma [mailto:sharmashalu.bio <at> gmail.com]
Sent: Wednesday, 24 April 2013 5:14 a.m.
To: Jason Stajich
Cc: Smithies, Russell; Fields, Christopher J; Peter Cock; shalabh sharma; bioperl-l <at> lists.open-bio.org
Subject: Re: [Bioperl-l] Taxa Id from blast report

Hi Jason,
             Thanks a lot for you suggestion. I tried that too but i am still not getting super kingdom, actually i don't
know how to put super kingdom in the database.
For example:
This is how i formatted my refseq microbial database:
makeblastdb -dbtype prot -in microbial_protein_mask.fasta -out refMicro -taxid_map GItaxa.txt
-parse_seqids     ( where GItaxa is the file <GI> <TaxonomyId><newline> ), there is no super kingdom.

So when i run this blast command:
blastx -query test.fas -db refMicro -max_target_seqs 1 -outfmt "6 staxids sscinames sskingdoms"
246200           N/A     N/A
246200           N/A     N/A

I would really appreciate you help.

Thanks
Shalu

On Fri, Apr 19, 2013 at 3:38 PM, Jason Stajich
<jason.stajich <at> gmail.com<mailto:jason.stajich <at> gmail.com>> wrote:
Did you provide -parse_seqids in the header?

Peter dealt with related things here:
http://blastedbio.blogspot.com/2012/10/my-ids-not-good-enough-for-ncbi-blast.html

Jason

On Apr 19, 2013, at 1:05 PM, shalu sharma
<sharmashalu.bio <at> gmail.com<mailto:sharmashalu.bio <at> gmail.com>> wrote:

Hi,
   Thanks everyone for you inputs.
 <at> Peter:
I got really excited when i saw that you can even get super kingdom, but
when i tried to test it i just got taxa ids but not the super kingdom. Do
you have any idea whats going wrong?
my command:
blastx  -query test.fas -db /db/ncbiblast/refseq/latest/refseq_protein
-max_target_seqs 1 -outfmt "6 staxids sskingdoms"

output:
246200    N/A
246200    N/A

Thanks
Shalu

On Thu, Apr 18, 2013 at 3:52 PM, Smithies, Russell <
Russell.Smithies <at> agresearch.co.nz<mailto:Russell.Smithies <at> agresearch.co.nz>> wrote:

I agree they have finally listened and added features requested by users
but I've been suggesting they have a compressed output format available
from eutils or genbank for years but have made no headway ;- (
What's so hard about gzip'ping the output? I'm sure it would go a long way
toward solving all the problems we get with truncated replies from queries!!

--Russell

-----Original Message-----
From: bioperl-l-bounces <at> lists.open-bio.org<mailto:bioperl-l-bounces <at> lists.open-bio.org> [mailto:
bioperl-l-bounces <at> lists.open-bio.org<mailto:bioperl-l-bounces <at> lists.open-bio.org>] On Behalf
Of Fields, Christopher J
Sent: Friday, 19 April 2013 6:26 a.m.
To: Peter Cock
Cc: bioperl-l <at> lists.open-bio.org<mailto:bioperl-l <at> lists.open-bio.org>; shalu sharma; shalabh sharma
Subject: Re: [Bioperl-l] Taxa Id from blast report

On Apr 18, 2013, at 11:48 AM, Peter Cock <p.j.a.cock <at> googlemail.com<mailto:p.j.a.cock <at> googlemail.com>>
wrote:

On Thu, Apr 18, 2013 at 5:32 PM, shalabh sharma
<shalabh.sharma7 <at> gmail.com<mailto:shalabh.sharma7 <at> gmail.com>> wrote:

Hey Peter,
     Thanks a lot, I really appreciate it. I wanted these things
implemented in blast from long time.

Thanks
Shalabh

Me too. You can get the descriptions from the plain text BLAST or XML
output already of course, but they're not so nice to work with.

Peter

NCBI has been much more receptive of user input over the last several
years, much more so than in the past.  I understand the reasoning for
dropping BLAST support (though there were definitely needless bumps in that
process).

chris

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