Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects use Bio::Align::Utilities qw(aa_to_dna_aln); my $dna_aln = aa_to_dna_aln($aaaln,\%dnaseqs); 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.

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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/ Email jason@bioperl.org Additional contributors names and emails here 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