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I have a contig which need to be blasted with all the databases under my /blast_db. Is there any parameter to do the job? Thanks,
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You can use blastdb_aliastool to make a database alias for all those dbs, then blast against that alias. So if you had nt and refseq_genomic in that folder, you'd cd into /blast_db and do
ThenCode:blastdb_aliastool -dblist "nt refseq_genomic" -dbtype nucl -out combined_db -title "Combined nt and refseq_genomic"
Code:blastn -db combined_db -query contigs.fa -out out.blast
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