Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects
use Bio::Align::Utilities qw(:all); # Even if the protein alignments are local make sure the start/end # stored in the LocatableSeq objects are to the full length protein. # The coding sequence that is passed in should still be the full # length CDS as the nt alignment will be generated. # %dnaseqs is a hash of CDS sequences (spliced) my $dna_aln = aa_to_dna_aln($aa_aln,\%dnaseqs); # The reverse, which is simpler. The input alignment has to be # translate-able, with gap lengths and an overall length divisible by 3 my $aa_aln = dna_to_aa_aln($dna_al); # Generate bootstraps my $replicates = bootstrap_replicates($aln,$count);
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
Title : dna_to_aa_aln Usage : my $aa_aln = dna_to_aa_aln($dna_aln); Function: Convert a DNA alignment to an amino acid alignment where the length of all alignment strings and the lengths of any gaps must be divisible by 3 Returns : Bio::Align::AlignI object Args : the DNA alignment, a Bio::Align::AlignI of DNA sequences
Title : bootstrap_replicates Usage : my $alns = &bootstrap_replicates($aln,100); Function: Generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from an alignment for the non-parametric bootstrap. Returns : Arrayref of L<Bio::SimpleAlign> objects Args : L<Bio::SimpleAlign> object Number of replicates to generate
Title : bootstrap_replicates_codons Usage : my $alns = &bootstrap_replicates_codons($aln,100); Function: Generate a pseudo-replicate of the data by randomly sampling, with replacement, the columns from a codon alignment for the non-parametric bootstrap. The alignment is assumed to start on the first position of a codon. Returns : Arrayref of L<Bio::SimpleAlign> objects Args : L<Bio::SimpleAlign> object Number of replicates to generate
Title : cat Usage : $aln123 = cat($aln1, $aln2, $aln3) Function : Concatenates alignment objects. Sequences are identified by id. An error will be thrown if the sequence ids are not unique in the first alignment. If any ids are not present or not unique in any of the additional alignments then those sequences are omitted from the concatenated alignment, and a warning is issued. An error will be thrown if any of the alignments are not flush, since concatenating such alignments is unlikely to make biological sense. Returns : A new Bio::SimpleAlign object Args : A list of Bio::SimpleAlign objects
Title : most_common_sequences Usage : @common = most_common_sequences ($align, $case_sensitivity) Function : Returns an array of the sequences that appear most often in the alignment (although this probably makes more sense when there is only a single most common sequence). Sequences are compared after removing any "-" (gap characters), and ambiguous units (e.g., R for purines) are only compared to themselves. The returned sequence is also missing the "-" since they don't actually make part of the sequence. Returns : Array of text strings. Arguments : Optional argument defining whether the comparison between sequences to find the most common should be case sensitive. Defaults to false, i.e, not case sensitive.