blastp commandline: against a protein database of a specific organism

Question

[Anushka]

Hello,

It is a very basic question regarding the -db option. I am using standalone blast+ and I want to blast my query.fasta ONLY against specific organism (e.g human) protein database only. I know blasting against refseq_protein/ swissprot are the usual choice

I am confused which database to select from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ .

How can I specify the specific organism in command line.

Thanks

[Kumar]

I am also search like this, did you get answer for that...

Thanks

Answer 1

[Siva]

You might want to check this thread: Vertebrate Subset Nr Database? Build My Own?

There is also information in BLAST Command Line Applications User Manual under the heading "Extract all human sequences from the nr database"

http://www.ncbi.nlm.nih.gov/books/NBK1763/

[Anushka]

Thanks Siva, that was very helpful

Answer 2

[hurfdurf]

Another alternative is to download all the peptide sequences using BioMart for your genome of interest.

Choose Ensembl Genes --> Homo Sapiens --> Sequences, then choose peptides, output to FASTA, and save. Then build locally as you would any other blast database. This will obviously miss heavily processed isoforms, so it depends what your application is.

[Anushka]

Thanks hurfdurf. I will definitely try this one.