Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER - Identify Protein Domains with HMMER
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'});
standard constructor addition
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
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
jw bargsten, <joachim.bargsten at wur.nl>
<joachim.bargsten at wur.nl>
To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Gonzales
CPAN shell
perl -MCPAN -e shell install Bio::Gonzales
For more information on module installation, please visit the detailed CPAN module installation guide.