Bio::SeqFeature::Similarity(3)             User Contributed Perl Documentation




NAME
       Bio::SeqFeature::Similarity - A sequence feature based on similarity

SYNOPSIS
           # obtain a similarity feature somehow
           print "significance: ", $sim_fea->significance(), "\n";
           print "bit score: ", $sim_fea->bits(), "\n";
           print "score: ", $sim_fea->score(), "\n";
           print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";

DESCRIPTION
       This module is basically a sequence features based on similarity, and
       therefore has support for measures assessing the similarity.

       Everything else is inherited from Bio::SeqFeature::Generic.

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 one of the Bioperl mailing lists.  Your participation is much
       appreciated.

         bioperl-lATbioperl.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-lATbioperl.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
       the bugs and their resolution.  Bug reports can be submitted via the
       web:

         http://bugzilla.open-bio.org/

AUTHOR - Hilmar Lapp
       Email hlappATgmx.net or hilmar.lappATpharma.com

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

   significance
        Title   : significance
        Usage   : $evalue = $obj->significance();
                  $obj->significance($evalue);
        Function:
        Returns :
        Args    :

   bits
        Title   : bits
        Usage   : $bits = $obj->bits();
                  $obj->bits($value);
        Function:
        Returns :
        Args    :

   frac_identical
        Title   : frac_identical
        Usage   : $fracid = $obj->frac_identical();
                  $obj->frac_identical($value);
        Function:
        Returns :
        Args    :

   seqlength
        Title   : seqlength
        Usage   : $len = $obj->seqlength();
                  $obj->seqlength($len);
        Function:
        Returns :
        Args    :

   seqdesc
        Title   : seqdesc
        Usage   : $desc = $obj->seqdesc();
                  $obj->seqdesc($desc);
        Function: At present this method is a shorthand for
                  $obj->annotation()->description().

                  Note that this is not stored in the tag system and hence will
                  not be included in the return value of gff_string().
        Returns :
        Args    :



perl v5.12.2                                                 February 24, 2011