NAME

Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects

SYNOPSIS

use Bio::Align::Utilities qw(aa_to_dna_aln);

my $dna_aln = aa_to_dna_aln($aaaln,\%dnaseqs);

DESCRIPTION

This module contains utility methods for manipulating sequence alignments ( Bio::Align::AlignI) objects.

The aa_to_dna_aln utility is essentially the same as the mrtrans program by Bill Pearson available at ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar. Of course this is a pure-perl implementation, but just to mention that if anything seems odd you can check the alignments generated against Bill's program.

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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

aa_to_dna_aln

 Title   : aa_to_dna_aln
 Usage   : my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs);
 Function: Will convert an AA alignment to DNA space given the 
           corresponding DNA sequences.  Note that this method expects 
           the DNA sequences to be in frame +1 (GFF frame 0) as it will
           start to project into coordinates starting at the first base of 
           the DNA sequence, if this alignment represents a different 
           frame for the cDNA you will need to edit the DNA sequences
           to remove the 1st or 2nd bases (and revcom if things should be).
 Returns : Bio::Align::AlignI object 
 Args    : 2 arguments, the alignment and a hashref.
           Alignment is a Bio::Align::AlignI of amino acid sequences. 
           The hash reference should have keys which are 
           the display_ids for the aa 
           sequences in the alignment and the values are a 
           Bio::PrimarySeqI object for the corresponding 
           spliced cDNA sequence. 

See also: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq