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  • Blasting your blastx results against your own database?

    Hi! I have .xml, .html, .art file results form a blastx. I need to blastp one of these files against an in-house database.
    Do you know which files (.xml, .html, or .art) I should blast?

    And what would the unix command be?

    blastp -db <in-house database.psq> -evalue 0.001 -i <file name> -o <file name>

    does that look right?

    Thanks I am very new to this all!

  • #2
    You need a BLAST database, usually created from a big FASTA file of all the target sequences with the makeblastdb command (or formatdb in the old legacy BLAST tool suite). A BLAST database is several files with a common name. The filenames will be name.p* for a protein database (including name.psq), and name.n* for a nucleotide database, but at the command line you just use the name without any extension. So probably:

    blastp -db <in-house database> -evalue 0.001 -i <file name> -o <file name>

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