NAME

FAST::Bio::Seq::GapSeqI - GapSeq interface, for gapped sequences

SYNOPSIS

            

              
              
$aa   = $gapseq->translate;
            
          

DESCRIPTION

This interface extends the FAST::Bio::SeqI interface to give additional functionality to gapped sequences.

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-l@bioperl.org                 - General discussion
http://bio.perl.org/MailList.html             - About the mailing lists
            
          

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 email or the web:

            

              
              
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
            
          

AUTHOR - Dave Ardell

Email dave.ardell@ebc.uu.se

Describe contact details here

APPENDIX

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

translate

            

              
              
Title   : translate
Usage   : $protein_seq_obj = $dna_seq_obj->translate
          #if full CDS expected:
          $protein_seq_obj = $cds_seq_obj->translate(undef,undef,undef,undef,1);
Function: Translate with gaps, so that an amino acid is aligned with the last base of a codon, even if said codon
          is interrupted by gaps. Generally this is only meaningful when input gaps are retained in the output; hence            the sequence is suitable for alignment to a DNA sequence. Otherwise, see pod for FAST::Bio::PrimarySeqI
Example : "UUUC--CC -> "--F----P"
Returns : a protein sequence object
Args    : none