Joachim Bargsten > Bio-Gonzales > Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER

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NAME ^

Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER - Identify Protein Domains with HMMER

SYNOPSIS ^

    use Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER;
    my $idfy =Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER->new({ domain_ids => [ 'id1', .., 'idn'], hmm_query_file => 'path/to/hmm/db'});

DESCRIPTION ^

METHODS ^

BUILD

standard constructor addition

$i->identify

Starts up hmmsearch and identifies putative domains.

Returns an array of hashes of the structure:

    [
        {
            file_name => 'file_name',
            domain_id => 'id',
            protein_id => 'id',
            from => x,
            to => y
        },
        ..
    ]

$i->unlink_destination_files

Deletes all destination files (the ones required in the constructor, except the cache file

_transform_hmm_hits

Transforms the best hits result from Bio::Gonzales::Util::SearchIO::HMMResult->get_best_hits to a more accessible structure and determines the maximum possible spanning region. This function also builds up a cache of sequence-id_size, found-domain and position cache for faster access later on

SEE ALSO =head1 AUTHOR ^

jw bargsten, <joachim.bargsten at wur.nl>

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