Search results for "distribution:FAST Bio::Symbol::Alphabet"
FAST::Bio::UnivAln - Bioperl alignment object
This module is the FAST::Bio::UnivAln alignment object which is part of the Bioperl project. Currently it has some nice methods for accessing an alignment after reading it in from certain formats, incl. utilities like consensus and reverse complement...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object
IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq objects from an ambiquous Seq object (containing non-standard characters given the meaning shown below) Extended DNA / RNA alphabet : (includes symbols for nucleotide ambiguity...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO::chadoxml - chadoxml sequence output stream
This object can transform FAST::Bio::Seq objects to chadoxml flat file databases (for chadoxml DTD, see http://gmod.cvs.sourceforge.net/gmod/schema/chado/dat/chado.dtd). This is currently a write-only module. $seqio = FAST::Bio::SeqIO->new(-file => '...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::SeqPattern - represent a sequence pattern or motif
FAST::Bio::Tools::SeqPattern module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"). FAST::Bio::Tools::SeqPattern is a concrete class that inherits from F...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::stockholm - stockholm sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC