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Question: blastn linux command specify database
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gravatar for chrisclarkson100
3.2 years ago by
chrisclarkson100 • 50
European Union
chrisclarkson100 • 50 wrote:

I'm trying to run a local linux blast search and I know the general formatof the command: blastx -query seqs.fasta -db nr -out output.blast.txt. However I don't know the short names for all the databases I want to search e.g. "ena_fun". How can I find these inputs out?

Thanks
blast • 4.0k views
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modified 3.2 years ago by Philipp Bayer ♦ 5.9k • written 3.2 years ago by chrisclarkson100 • 50
1
gravatar for Philipp Bayer
3.2 years ago by
Philipp Bayer ♦ 5.9k
Australia/Perth/UWA
Philipp Bayer ♦ 5.9k wrote:

You have two avenues to choose:

1. You run BLAST locally, but use a remote database using the flag -remote. In that case, you can choose a database from this list

(link via List of NCBI database names for standalone BLAST remote search )

2. You run BLAST locally with a local database. In that case, you can use any protein/nucleotide file. You need to format it using

    makeblastdb -dbtype prot/nucl (depends on whether you have proteins or nucleotides) -in your_filename

Then you can use the name of the file you used for makeblastdb as argument for the -db flag in blastx.
ADD COMMENT • link written 3.2 years ago by Philipp Bayer ♦ 5.9k
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