Command Line BLAST for specific genome using TAXID

[eatashpaz]

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.

[DeNovoG]

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. I´ve 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!

[sklages]

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