Bio::SearchIO::hmmer(3pm)				User Contributed Perl Documentation				 Bio::SearchIO::hmmer(3pm)

NAME

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

SYNOPSIS

	   # 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(), "
";
	       while( my $hit = $result->next_hit ) {
		   print $hit->name(), "
";
		   while( my $hsp = $hit->next_hsp ) {
		       print "length is ", $hsp->length(), "
";
		   }
	       }
	   }

DESCRIPTION

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Kai Blin
       Email kai.blin-at-biotech.uni-tuebingen.de

APPENDIX

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

perl v5.14.2							    2012-03-02						 Bio::SearchIO::hmmer(3pm)