Search results for "distribution:FAST Bio::SeqI"
FAST::Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
FAST::Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guarenteed to get for any FAST::Bio::SeqI - for most users of the package the documentation (and methods) in this class are not at useful - thi...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::DB::SeqI - Abstract Interface for Sequence databases
Abstract interface for a sequence database...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::MySeqI - Abstract Interface of Sequence (with features)
SeqI is the abstract interface of annotated Sequence. These methods are those which you can be guarenteed to get for any annseq. There aren't many here, because too many complicated functions here prevent implementations which are just wrappers aroun...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
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::Seq::MetaI - Interface for sequence objects with residue-based meta information
This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, seq...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::QualI - Interface definition for a FAST::Bio::Seq::Qual
This object defines an abstract interface to basic quality information. PrimaryQual is an object just for the quality and its name(s), nothing more. There is a pure perl implementation of this in FAST::Bio::Seq::PrimaryQual. If you just want to use F...
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::SeqFeatureI - Abstract interface of a Sequence Feature
This interface is the functions one can expect for any Sequence Feature, whatever its implementation or whether it is a more complex type (eg, a Gene). This object does not actually provide any implementation, it just provides the definitions of what...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::TraceI - Interface definition for a FAST::Bio::Seq::Trace
This object defines an abstract interface to basic trace information. This information may have come from an ABI- or scf- formatted file or may have been made up....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
This interface extends the FAST::Bio::SeqI interface to give additional functionality to sequences with richer data sources, in particular from database sequences (EMBL, GenBank and Swissprot). For a general implementation, please see the documentati...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::LargeSeqI - Interface class for sequences that cache their residues in a temporary file
The interface class defines a group of sequence classes that do not keep their sequence information in memory but store it in a file. This makes it possible to work with very large files even with limited RAM. The most important consequence of file c...
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::SeqAnalysisParserI - Sequence analysis output parser interface
SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence analysis in this sense is a search for similarities or the identification of features on the sequence, like a databank search or a a gene prediction r...
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::SeqFeature::Gene::TranscriptI - Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
A feature representing a transcript....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene
A feature representing a gene structure....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq - Sequence object, with features
A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqIO - Handler for SeqIO Formats
FAST::Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, FAST::Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The FAST::Bio::SeqIO system can be thought of lik...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are FAST::Bio::LocatableSeq objects with additional methods to store that meta information. See FAST::Bio::LocatableSeq and FAST::B...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::LocatableSeq - A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
The LocatableSeq sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC