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  • Blastall help !!!

    Hello All,

    I need some help in optimizing my blastall query. I have a file of 10000 genes, and i wanted to blast them against themselves. So, i created blast db to perform blastall. But i dont want the genes that map to themselves. I would like to get second best hit from the results. Can i do this in blastall using some parameters or do i need to write a perl script for this?

    Code:
    blastall -p blastn -m 9 -d testgenesdb -i test.fasta -o outputtest.QUERY
    That is the query i uses and it brings out blast results in tabular format..
    please help me if u know optimizing blast queries.

    Thank you all

  • #2
    example

    code exclude_self.pl

    while (<STDIN>)
    {
    my @l= split(/\t/,$_);
    if ($l[0] ne $l[1])
    {
    print join("\t",@l)."\n";
    }
    }


    --

    perl exclude_self.pl < outputtest.QUERY > outputtest.QUERY.noself

    Something like this should work.

    best,
    Klaas

    Comment


    • #3
      Thank you for the code.. this is what i wanted but i need only second best hit.. i dont want all the results...how can i achieve it?
      Last edited by empyrean; 03-10-2011, 08:12 PM.

      Comment


      • #4
        How to get the second best hit or after running above code, i need the first row with best evalue for all the combinations..

        Comment

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