Search results for "distribution:BioPerl Bio::SeqFeature"
Bio::SeqFeature::Lite - Lightweight Bio::SeqFeatureI class
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in Bio::SeqFeatureI with the following additions: The new() ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::SubSeq - Feature representing a subsequence
Bio::SeqFeature::SubSeq extends Bio::SeqFeature::Generic features to represent a subsequence. When this feature is attached to a template sequence, the sequence of feature is the subsequence of the template at this location. The purpose of this class...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Primer - Primer Generic SeqFeature
This module handles PCR primer sequences. The Bio::SeqFeature::Primer object is a Bio::SeqFeature::Subseq object that can additionally contain a primer sequence and its coordinates on a template sequence. The primary_tag() for this object is 'Primer'...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Generic - Generic SeqFeature
Bio::SeqFeature::Generic is a generic implementation for the 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 example, this is f...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqFeature::Amplicon - Amplicon feature
Bio::SeqFeature::Amplicon extends Bio::SeqFeature::Subseq to represent an amplicon sequence and optional primer sequences....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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::SeqFeature::Collection - A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.
This object will efficiently allow one for query subsets of ranges within a large collection of sequence features (in fact the objects just have to be Bio::RangeI compliant). This is done by the creation of bins which are stored in order in a B-Tree ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::SeqFeature::Generic....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 ...
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::Computation - Computation SeqFeature
Bio::SeqFeature::Computation extends the Generic seqfeature object with a set of computation related fields and a more flexible set of storing more types of score and subseqfeatures. It is compatible with the Generic SeqFeature object. The new way of...
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::PositionProxy - handle features when truncation/revcom sequences span a feature
PositionProxy is a Proxy Sequence Feature to handle truncation and revcomp without duplicating all the data within the sequence features. It holds a new location for a sequence feature and the original feature it came from to provide the additional a...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::SeqFeature::FeaturePair and therefore implements Bio::SeqFeatureI, whereas the two features of the pair are descendants of Bio::SeqFeature::Generic, w...
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::Tools::IDHandler - maps $seq_feature-gtprimary_tag
Class to map $seq_feature->primary_tag...
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