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

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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:

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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