NAME

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

SYNOPSIS

  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);

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:

  https://github.com/bioperl/bioperl-live/issues

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

dna_to_aa_aln

 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

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

bootstrap_replicates_codons

 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

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

most_common_sequences

 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.