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 listsSupport
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/issuesAUTHOR - 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 sequencesSee 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 generatebootstrap_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 generatecat
Title : cat
Usage : $aln123 = cat($aln1, $aln2, $aln3)
Function : Concatenates alignment objects. Sequences are identified by id.
An error will be thrown if the sequence ids are not unique in the
first alignment. If any ids are not present or not unique in any
of the additional alignments then those sequences are omitted from
the concatenated alignment, and a warning is issued. An error will
be thrown if any of the alignments are not flush, since
concatenating such alignments is unlikely to make biological
sense.
Returns : A new Bio::SimpleAlign object
Args : A list of Bio::SimpleAlign objectsmost_common_sequences
Title : most_common_sequences
Usage : @common = most_common_sequences ($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.