Bio::Align::Utilities.3pm

Langue: en

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

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