Bio::Align::Utilities(3pm)				User Contributed Perl Documentation				Bio::Align::Utilities(3pm)

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

perl v5.14.2							    2012-03-02						Bio::Align::Utilities(3pm)