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:
https://redmine.open-bio.org/projects/bioperl/
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