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  • scami
    Member
    • Sep 2010
    • 55
    #1

    Search specific blast database regions

    Hi there,

    I am using blastn in command line. I have a genome and created a blast database out of it with makeblastdb
    During the pipeline I am developing I need to blast some sequence versus specific chromosomes of the genome and not the entire genome. At the moment I use the command

    blastn -query queryFile -db genomeDatabase -outfmt 6

    Let's say that in the genomeDatabase file I have chr1, chr2, chr3 and so on. What can I add to my command to search my sequence versus just chr1 or chr2 and so on?
    thanks for your help!
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