Question: blastp commandline: against a protein database of a specific organism
0
gravatar for Anushka
4.4 years ago by
Anushka20
France
Anushka20 wrote:

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

 

 

 

 

 

ADD COMMENTlink modified 4.4 years ago by hurfdurf460 • written 4.4 years ago by Anushka20

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

Thanks

ADD REPLYlink written 3.8 years ago by Manoj30
1
gravatar for Siva
4.4 years ago by
Siva1.6k
United States
Siva1.6k wrote:

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/

 

ADD COMMENTlink written 4.4 years ago by Siva1.6k

Thanks Siva, that was very helpful

ADD REPLYlink written 4.4 years ago by Anushka20
1
gravatar for hurfdurf
4.4 years ago by
hurfdurf460
United States
hurfdurf460 wrote:

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.

ADD COMMENTlink written 4.4 years ago by hurfdurf460

Thanks hurfdurf. I will definitely try this one.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Anushka20
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