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Old 05-30-2013, 07:22 PM   #1
SDPA_Pet
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Default BLASTN output format

Hi, is it possible to let blastn output show taxa name, such as E.coli, not just Gene bank ID.

If it is possible, what parameter should I use.

Thanks
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Old 05-30-2013, 11:11 PM   #2
rhinoceros
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Quote:
Originally Posted by SDPA_Pet View Post
Hi, is it possible to let blastn output show taxa name, such as E.coli, not just Gene bank ID.

If it is possible, what parameter should I use.

Thanks
It's possible at least with local blast 2.2.28+. However, in addition to nt/nr/refseq db you need to install ncbi taxdb properly (available here). Read more from here too..

concrete example:

blastn -query file.fasta -db refseq_genomic -outfmt '6 qseqid sseqid pident length evalue sscinames'

Last edited by rhinoceros; 05-31-2013 at 01:37 AM.
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Old 05-31-2013, 05:24 AM   #3
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Hi Thanks.

Are you sure this is right -outfmt '6 qseqid sseqid pident length evalue sscinames' ? Should it be -outfmt 6 'qseqid sseqid pident length evalue sscinames' ?

Which parameter will control the name? "sscinames"
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Old 05-31-2013, 05:27 AM   #4
rhinoceros
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Originally Posted by SDPA_Pet View Post
Hi Thanks.

Are you sure this is right -outfmt '6 qseqid sseqid pident length evalue sscinames' ? Should it be -outfmt 6 'qseqid sseqid pident length evalue sscinames' ?
As I wrote it works fine.

Quote:
Which parameter will control the name? "sscinames"
Yes. Check here for other flags. Remember, it will not work unless taxdb has been setup properly..
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Old 06-02-2013, 09:21 AM   #5
SDPA_Pet
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Hi, I installed the taxa.db and ran the blastn against nt database. The results are what I want.

I also need to blast against RDP database which I created the from a fasta filed download on RDP database (http://rdp.cme.msu.edu/misc/resource...52486.spitfire). I try to do the same way as I did for nt database, but it won't give me the taxa name. What should I do?

Thank you,

Last edited by SDPA_Pet; 06-02-2013 at 10:02 AM.
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Old 06-02-2013, 12:28 PM   #6
GenoMax
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In order to use the "taxdb" data you will probably need to run the blast search against "16SMicrobial" set available from NCBI. I would guess that the taxdb data is only limited to blast indexes available from NCBI.
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Old 06-03-2013, 01:29 AM   #7
rhinoceros
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Quote:
Originally Posted by SDPA_Pet View Post
Hi, I installed the taxa.db and ran the blastn against nt database. The results are what I want.

I also need to blast against RDP database which I created the from a fasta filed download on RDP database (http://rdp.cme.msu.edu/misc/resource...52486.spitfire). I try to do the same way as I did for nt database, but it won't give me the taxa name. What should I do?

Thank you,
Doesn't RDP provide tools for taxa assignment?
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Old 06-03-2013, 07:27 AM   #8
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I don't know. I download the fasta format and convert to NCBI database. I blast against it, but no taxa assignment.
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Old 06-03-2013, 09:23 AM   #9
para_seq
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I wonder why you want to blast RDP database for taxonomic assignment instead of using RDP Classifier, which has become a standard way for this task.
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Old 06-03-2013, 02:18 PM   #10
kmcarr
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Quote:
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I don't know. I download the fasta format and convert to NCBI database. I blast against it, but no taxa assignment.
The taxonomy assignment in BLAST is only going to work when you are blasting against an NCBI database (e.g. nr, nt, RefSeq, etc.). BLAST uses the NCBI gi numbers to link the entries in the taxonomy database to the the entries in the BLAST database.
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Old 06-05-2013, 08:47 PM   #11
A_Morozov
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If you want to do a taxonomic assignment for ribosomal RNAs (metagenome or something), look at mothur package instead of BLAST. You will not have to parse results manually or write the script or whatever - a couple commands in mothur and you have a nice list of taxa, along with how many sequences went to every taxon and which ones exactly. Not sure about the algorithms it uses, but it does its job well enough in our experience.
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