Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


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 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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Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

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