Search results for "dist:FAST ACID"
FAST::Bio::GapSeqI - GapSeq interface, for gapped sequences
This interface extends the FAST::Bio::SeqI interface to give additional functionality to gapped sequences....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqUtils - Additional methods for PrimarySeq objects
This class is a holder of methods that work on FAST::Bio::PrimarySeqI- compliant sequence objects, e.g. FAST::Bio::PrimarySeq and FAST::Bio::Seq. These methods are not part of the FAST::Bio::PrimarySeqI interface and should in general not be essentia...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
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::PrimarySeqI - Interface definition for a FAST::Bio::PrimarySeq
This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers-only class which defines what methods have to be implmented by...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::MyPrimarySeqI - Interface definition for a FAST::Bio::PrimarySeq
This object defines an abstract interface to basic sequence information. PrimarySeq is an object just for the sequence and its name(s), nothing more. Seq is the larger object complete with features. There is a pure perl implementation of this in FAST...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::SeqStats - Object holding statistics for one particular sequence
FAST::Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create t...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::CodonTable - Codon table object
Codon tables are also called translation tables or genetic codes since that is what they represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. CodonT...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Tools::MySeqStats - Object holding statistics for one particular sequence
FAST::Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create t...
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::Search::Hit::HitI - Interface for a hit in a similarity search result
FAST::Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::PullHitI - FAST::Bio::Search::Hit::HitI interface for pull parsers.
This object handles the hit data from a database sequence search. PullHitI is for fast implementations that only do parsing work on the hit data when you actually request information by calling one of the HitI methods. Many methods of HitI are implem...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::Exon - a feature representing an exon
This module implements a feature representing an exon by implementing the FAST::Bio::SeqFeature::Gene::ExonI interface. By default an Exon is coding. Supply -is_coding => 0 to the constructor or call $exon->is_coding(0) otherwise. Apart from that, th...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::ExonI - Interface for a feature representing an exon
A feature representing an exon. An exon in this definition is transcribed and at least for one particular transcript not spliced out of the pre-mRNA. However, it does not necessarily code for amino acid....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Search::Hit::GenericHit - A generic implementation of the FAST::Bio::Search::Hit::HitI interface
This object handles the hit data from a Database Sequence Search such as FASTA or BLAST. Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects ar...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::NC_Feature - superclass for non-coding features
Describe the object here...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC