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  • How could blast contig with multiple databases?

    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,

  • #2
    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
    Code:
    blastdb_aliastool -dblist "nt refseq_genomic" -dbtype nucl -out combined_db -title "Combined nt and refseq_genomic"
    Then
    Code:
    blastn -db combined_db -query contigs.fa -out out.blast

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