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bio::tools::promoterwise(3pm) [debian man page]

Bio::Tools::Promoterwise(3pm)				User Contributed Perl Documentation			     Bio::Tools::Promoterwise(3pm)

NAME

       Bio::Tools::Promoterwise - parser for Promoterwise tab format output

SYNOPSIS

	 use Bio::Tools::Promoterwise;

	 my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
						-query1_seq=>$seq1,
						-query2_seq=>$seq2);
	 while (my $fp = $pw->next_result){
	   print "Hit Length: ".$fp->feature1->length."
";
	   print "Hit Start: ".$fp->feature1->start."
";
	   print "Hit End: ".$fp->feature1->end."
";
	   print "Hsps: 
";
	   my @first_hsp = $fp->feature1->sub_SeqFeature;
	   my @second_hsp = $fp->feature2->sub_SeqFeature;
	   foreach my $i (0..$#first_hsp){
	     print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
		   $second_hsp[$i]->start. " ".$second_hsp[$i]->end."
";
	   }
	 }

DESCRIPTION

       Promoteriwise is an alignment algorithm that relaxes the constraint that local alignments have to be co-linear. Otherwise it provides a
       similar model to DBA, which is designed for promoter sequence alignments.  Promoterwise is written by Ewan Birney.  It is part of the wise2
       package available at <ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/>

       This module is the parser for the Promoterwise output in tab format.

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 - Shawn Hoon
       Email shawnh@fugu-sg.org

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Promoterwise->new();
	Function: Builds a new Bio::Tools::Promoterwise object
	Returns : L<Bio::Tools::Promoterwise>
	Args	: -fh/-file => $val, # for initing input, see Bio::Root::IO

   next_result
	Title	: next_result
	Usage	: my $r = $rpt_masker->next_result
	Function: Get the next result set from parser data
	Returns : an  L<Bio::SeqFeature::FeaturePair>
	Args	: none

perl v5.14.2							    2012-03-02					     Bio::Tools::Promoterwise(3pm)

Check Out this Related Man Page

Bio::Tools::Tmhmm(3pm)					User Contributed Perl Documentation				    Bio::Tools::Tmhmm(3pm)

NAME

       Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)

SYNOPSIS

	 use Bio::Tools::Tmhmm;
	 my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle );
	 while ( my $tmhmm_feat = $parser->next_result ) {
	    # do something, e.g.
	    push @tmhmm_feat, $tmhmm_feat;
	 }

DESCRIPTION

       TMHMM is software for the prediction of transmembrane helices in proteins.  See	<http://www.cbs.dtu.dk/services/TMHMM/> for more details.

       This module parses the "long output" format of TMHMM 2.0 and creates a Bio:SeqFeature::Generic object for each "TMHelix" feature found from
       lines like this:

	 my_sequence_id  TMHMM2.0  TMhelix     54    76

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 - Torsten Seemann
       Email torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - Bala
       Email savikalpa@fugu-sg.org

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Tmhmm->new();
	Function: Builds a new Bio::Tools::Tmhmm object
	Returns : Bio::Tools::Tmhmm
	Args	: Either of the following as per L<Bio::Root::IO> interface
		    -fh   => $filehandle
		    -file => $filename

   next_result
	Title	: next_result
	Usage	: my $feat = $Tmhmm->next_result
	Function: Get the next result set from parser data
	Returns : Bio::SeqFeature::Generic
	Args	: none

perl v5.14.2							    2012-03-02						    Bio::Tools::Tmhmm(3pm)
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