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


  use Bio::Align::Utilities qw(:all);
  # %dnaseqs is a hash of CDS sequences (spliced)

  # 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.
  my $dna_aln = &aa_to_dna_aln($aa_aln,\%dnaseqs);

  # 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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AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org


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. 

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


 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     : 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
 Returns   : A new Bio::SimpleAlign object
 Args      : A list of Bio::SimpleAlign objects