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  • bio_informatics
    Senior Member
    • Nov 2013
    • 182

    #1

    Stuck at blast in Bio perl

    Hi All,
    I am newbie in bio perl.
    I want to blast a sequence using, standAloneBlast and parse its output later.
    I have my blast+ installed and has been added to PATH.

    Now, here is the mystery.
    How do I proceed? What should be done?
    I have browsed many posts but was unable to understand how and what they are doing

    Code:
    my $in = Bio::SeqIO->new (-format=>'blast',-file=>$fasta_file);
    what this will lead me to?
    Next I tried
    Code:
    while(my $result= $in->next_result){
          ##I cannot get next_result
    }
    OS: Ubuntu 12.04
    However, on command line, we build database by running a sequence against another file or database, and then blast is run.
    How is the case in Bio Perl?

    Please help me understand this.
    Bioinformaticscally calm

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