Home
Reading
Searching
Subscribe
Sponsors
Statistics
Posting
Contact
Spam
Lists
Links
About
Hosting
Filtering
Features Download
Marketing
Archives
FAQ
Blog
 
Gmane
From: shalu sharma <sharmashalu.bio <at> gmail.com>
Subject: Re: Taxa Id from blast report
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 23rd April 2013 17:14:04 UTC (over 3 years ago)
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 
 ), 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
<[email protected]>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 
> wrote:
>
> Hi,
>    Thanks everyone for you inputs.
> @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 <
> [email protected]> 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: [email protected] [mailto:
> [email protected]] On Behalf Of Fields, Christopher J
> Sent: Friday, 19 April 2013 6:26 a.m.
> To: Peter Cock
> Cc: [email protected]; shalu sharma; shalabh sharma
> Subject: Re: [Bioperl-l] Taxa Id from blast report
>
> On Apr 18, 2013, at 11:48 AM, Peter Cock 
> wrote:
>
> On Thu, Apr 18, 2013 at 5:32 PM, shalabh sharma
>  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
>
>
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Bioperl-l mailing list
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> Jason Stajich
> [email protected]
> [email protected]
>
>
 
CD: 3ms