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Geneious 4.5.4 (Default branch)
01-28-2009
Geneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as linear and circular DNA sequences, proteins, phylogenies, chromatograms, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, restriction analysis, contig assembly, access to biological databases at NCBI and elsewhere (PubMed, Nucleotide, PopSet, SNP, Structure, PFAM, etc.), BLAST, and more. It includes an API for creating your own plugins.License: Other/Proprietary License with Free TrialChanges:|
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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)