Question: blastn linux command specify database
gravatar for chrisclarkson100
5.3 years ago by
European Union
chrisclarkson10090 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?


blast • 5.8k views
ADD COMMENTlink modified 5.3 years ago by Philipp Bayer6.9k • written 5.3 years ago by chrisclarkson10090
gravatar for Philipp Bayer
5.3 years ago by
Philipp Bayer6.9k
Philipp Bayer6.9k 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 COMMENTlink modified 15 months ago by Ram32k • written 5.3 years ago by Philipp Bayer6.9k
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