Search results for "dist:FAST Bio::SeqFeature"
FAST::Bio::SeqFeature::Generic - Generic SeqFeature
FAST::Bio::SeqFeature::Generic is a generic implementation for the FAST::Bio::SeqFeatureI interface, providing a simple object to provide all the information for a feature on a sequence. For many Features, this is all you will need to use (for exampl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Similarity - A sequence feature based on similarity
This module is basically a sequence features based on similarity, and therefore has support for measures assessing the similarity. Everything else is inherited from FAST::Bio::SeqFeature::Generic....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::FeaturePair - hold pair feature information e.g. blast hits
A sequence feature object where the feature is itself a feature on another sequence - e.g. a blast hit where residues 1-40 of a protein sequence SW:HBA_HUMAN has hit to bases 100 - 220 on a genomic sequence HS120G22. The genomic sequence coordinates ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::SimilarityPair - Sequence feature based on the similarity of two sequences.
Lightweight similarity search result as a pair of Similarity features. This class inherits off FAST::Bio::SeqFeature::FeaturePair and therefore implements FAST::Bio::SeqFeatureI, whereas the two features of the pair are descendants of FAST::Bio::SeqF...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region that is part of a transcriptional unit
A UTR is a FAST::Bio::SeqFeature::Gene::ExonI compliant object that is non-coding, and can be either 5' or 3' in a transcript....
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::SeqFeature::Gene::Intron - An intron feature
Describe the object here...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::Promoter - Describes a promoter
Describe the object here...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-gtprimary_tag
Class to map $seq_feature->primary_tag...
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
FAST::Bio::SeqFeature::Gene::Transcript - A feature representing a transcript
A feature representing a transcript....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature-gtprimary_tag
This class implements an object for mapping between types; for example, the types in a genbank feature table, and the types specified in the Sequence Ontology. You can specify your own mapping, either as a simple hash index, or by providing your own ...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Gene::Poly_A_site - poly A feature
Inherits from FAST::Bio::SeqFeature::Gene::NC_Feature....
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::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
FAST::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 FAST::Bio::SeqFeature::Gene::TranscriptI (interface) and FAST::Bio::SeqFeature::Gene::Transcript (implementation) for the features of...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::SeqFeature::Tools::FeatureNamer - generates unique persistent names for features
This is a helper class for providing names for SeqFeatures The FAST::Bio::SeqFeatureI class provides a display_name method. Typically the display_name is not set when parsing formats such as genbank - instead properties such as label, product or gene...
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::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