Search results for "dist:BioPerl GENE"
Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit
A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is non-coding, and can be either 5' or 3' in a transcript....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::Exon - a feature representing an exon
This module implements a feature representing an exon by implementing the 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, this cla...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Prediction::Gene - a predicted gene structure feature
A feature representing a predicted gene structure. This class actually inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that functionality, plus a few methods supporting predicted sequence features, like a predicted CDS and a pred...
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::Intron - An intron feature
Describe the object here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::Promoter - Describes a promoter
Describe the object here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::NC_Feature - superclass for non-coding features
Describe the object here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::Transcript - A feature representing a transcript
A feature representing a transcript....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Gene::Poly_A_site - poly A feature
Inherits from Bio::SeqFeature::Gene::NC_Feature....
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::GeneStructure - A feature representing an arbitrarily complex structure of a gene
A feature representing a gene structure. As of now, a gene structure really is only a collection of transcripts. See Bio::SeqFeature::Gene::TranscriptI (interface) and Bio::SeqFeature::Gene::Transcript (implementation) for the features of such object...
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::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 Bio::Prim...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::DasI - DAS-style access to a feature database
Bio::DasI is a simplified alternative interface to sequence annotation databases used by the distributed annotation system (see Bio::Das). In this scheme, the genome is represented as a series of features, a subset of which are named. Named features ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO - Handler for SeqIO Formats
Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for u...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::MZEF - Results of one MZEF run
The MZEF module provides a parser for MZEF gene structure prediction output. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::OntologyIO - Parser factory for Ontology formats
This is the parser factory for different ontology sources and formats. Conceptually, it is very similar to Bio::SeqIO, but the difference is that the chunk of data returned as an object is an entire ontology....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Grail - Results of one Grail run
The Grail module provides a parser for Grail gene structure prediction output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::kegg - KEGG sequence input/output stream
This class transforms KEGG gene records into Bio::Seq objects. Mapping of record properties to object properties This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC