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
1 answer
You have two avenues to choose:
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 )
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_filenameThen you can use the name of the file you used for
makeblastdbas argument for the-dbflag in blastx.
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