/ 
Bio-Gonzales-0.083
River stage zero No dependents
/ Bio::Gonzales::Domain::Identification::HMMER

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
    },
    ..
]

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>