blastn linux command specify database

Question

[chrisclarkson100]

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

Answer 1

[Philipp Bayer]

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.