Search results for "dist:FAST Bio::Symbol::Symbol"
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::swiss - Swissprot sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from Swiss-Pprot flat file databases. There is a lot of flexibility here about how to dump things which needs to be documented. GN (Gene name) line management details A Uniprot/Swiss-Prot entry ...
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::SeqIO::entrezgene - Entrez Gene ASN1 parser
This is EntrezGene ASN bioperl parser. It is built on top of FAST::Bio::ASN1::EntrezGene, a low level ASN parser built by Mingyi Liu (<http://sourceforge.net/projects/egparser>). The easiest way to use it is shown above. You will get most of the Entr...
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
FAST::Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this. Unless you're writing a parser, you won't eve...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Tools::Unflattener - turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Most GenBank entries for annotated genomic DNA contain a flat list of features. These features can be parsed into an equivalent flat list of FAST::Bio::SeqFeatureI objects using the standard FAST::Bio::SeqIO classes. However, it is often desirable to...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC