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Old 11-01-2011, 06:23 PM   #1
eatashpaz
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Location: College Station

Join Date: Nov 2011
Posts: 1
Question Command Line BLAST for specific genome using TAXID

I am using command line blast in MS-DOS and I can easily use it for NCBI database NT. My problem is in doing BLAST for a FASTA file against a specific genome:
  • viral genome
  • bacterial genome
  • fungal genome

I have the TAXID for each group and although I know how to do it using online BLAST, my problem is in limiting the database to just a specific taxid I have in Command Line BLAST in MS-DOS.

I would be delighted if you help me in this case.
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Old 02-10-2012, 09:26 AM   #2
DeNovoG
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Location: South America

Join Date: May 2010
Posts: 7
Question same question here, any updates since your last post?

I am trying to blast my sanger fastq reads originated from BACs to filter contaminants against the e.coli genomes database. Ive downloaded some of the most representative but it will be more practical to blast against an updated nt database using blast+ on my local server, in this case I want to blast against the nt taxId:562 (e.coli).
Do you know if there is a way of doing this maybe by creating an alias for the nt database or if there is a way of extracting a subset DB by taxid and creating a new blast DB from the nt?

any help or comment would be greatly appreciated

Best Regards!

Last edited by DeNovoG; 02-10-2012 at 09:29 AM.
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Old 02-10-2012, 12:18 PM   #3
sklages
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Default

Maybe as a starting point, http://nebc.nerc.ac.uk/tools/code-co...#-tax2blast-pl
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