/ 
bioperl-1.5.2_004-RCf
/ Bio::Align::Utilities

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

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@bioperl.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