Search results for "distribution:BioPerl Bio::SeqI"
Bio::SeqI - [Developers] Abstract Interface of Sequence (with features)
Bio::SeqI is the abstract interface of annotated Sequences. These methods are those which you can be guaranteed to get for any Bio::SeqI. For most users of the package the documentation (and methods) in this class are not at useful - this is a develo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::SeqI - Abstract Interface for Sequence databases
Abstract interface for a sequence database...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::PrimarySeqI - Interface definition for a 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 implemented b...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::UpdateableSeqI - Descendant of Bio::SeqI that allows updates
Bio::UpdateableSeqI is an interface for Sequence objects which are expected to allow users to perform basic editing functions (update/delete) on their component SeqFeatures....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::QualI - Interface definition for a 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 Bio::Seq::PrimaryQual. If you just want to use Bio::Se...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::TraceI - Interface definition for a 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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::RichSeqI - interface for sequences from rich data sources, mostly databases
This interface extends the 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 documentation for...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::WebDBSeqI - Object Interface to generalize Web Databases for retrieving sequences
Provides core set of functionality for connecting to a web based database for retrieving sequences. Users wishing to add another Web Based Sequence Dabatase will need to extend this class (see Bio::DB::SwissProt or Bio::DB::NCBIHelper for examples) a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DB::UpdateableSeqI - An interface for writing to a database of sequences.
This module seeks to provide a simple method for pushing sequence changes back to a Sequence Database - which can be an SQL compliant database, a file based database, AceDB, etc....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::CollectionI - An interface for a collection of SeqFeatureI objects.
This interface describes the basic methods needed for a collection of Sequence Features....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::TypedSeqFeatureI - a strongly typed SeqFeature
This interface describes the extension of SeqFeatureI to being a strongly typed SeqFeature. Bio::SeqFeature::TypedSeqFeatureI extends the Bio::SeqFeatureI interface (ie, a TypedSeqFeatureI feature must also implement all the Bio::SeqFeatureI interfac...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily complex structure of a gene
A feature representing a gene structure....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable of creating SeqAnalysisParserI compliant parsers
This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See Bio::SeqA...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp
This object stores a sequence as a series of files in a temporary directory. The aim is to allow someone the ability to store very large sequences (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real memory machine!)....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC