Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)


    # do not use this class directly it is available through Bio::SearchIO
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer',
                               -file   => 't/data/L77119.hmmer');
    while( my $result = $in->next_result ) {
        # this is a Bio::Search::Result::HMMERResult object
        print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
        while( my $hit = $result->next_hit ) {
            print $hit->name(), "\n";
            while( my $hsp = $hit->next_hsp ) {
                print "length is ", $hsp->length(), "\n";


This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3


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AUTHOR - Kai Blin



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _