Bio::Align::Utilities(3)

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

SYNOPSIS
  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);

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/wiki/Mailing_lists  - About the mailing lists

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

bioperl-l@bioperl.org

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:

  http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org

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

  bootstrap_replicates
 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

  cat
 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