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=head1 NAME
sequence_codon module - part of the Wise2 package
=head1 SYNOPSIS
This module contains helper functions for the Wise2 package
=head1 DESCRIPTION
=over
=item reverse_complement_Sequence
&Wise2::reverse_complement_Sequence(seq)
This both complements and reverses a sequence,
- a common wish!
The start/end are correct with respect to the start/end
of the sequence (ie start = end, end = start).
Argument seq [READ ] Sequence to that is used to reverse (makes a new Sequence) [Sequence *]
Return [OWNER] new Sequence which is reversed [Sequence *]
=item magic_trunc_Sequence
&Wise2::magic_trunc_Sequence(seq,start,end)
Clever function for dna sequences.
When start < end, truncates normally
when start > end, truncates end,start and then
reverse complements.
ie. If you have a coordinate system where reverse
sequences are labelled in reverse start/end way,
then this routine produces the correct sequence.
Argument seq [READ ] sequence that is the source to be truncated [Sequence *]
Argument start [READ ] start point [int]
Argument end [READ ] end point [int]
Return [OWNER] new Sequence which is truncated/reversed [Sequence *]
=item translate_Sequence
&Wise2::translate(dna,ct)
This translates a DNA sequence to a protein.
It assumes that it starts at first residue
(use trunc_Sequence to chop a sequence up).
Argument dna [READ ] DNA sequence to be translated [Sequence *]
Argument ct [READ ] Codon table to do codon->aa mapping [CodonTable *]
Return [OWNER] new protein sequence [Sequence *]
=back
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