Module:Bio::Seq

From BioPerl
Jump to: navigation, search
Bio::Seq
PDoc Bio::Seq
CPAN Bio::Seq
metaCPAN Bio::Seq


A Seq object is a sequence with sequence features placed on it. The Seq object contains a Bio::PrimarySeq object for the actual sequence and also implements its interface, Bio::PrimarySeqI.

Overview

In Bioperl we have 3 main players that people are going to use frequently:

Bio::PrimarySeq 
just the sequence and its names, nothing else. e.g. a fasta file of a sequence.
Bio::SeqFeatureI 
a feature on a sequence, potentially with a sequence and a location and annotation. e.g. a single entry in an EMBL/GenBank/DDBJ feature table
Bio::Seq 
A sequence and a collection of sequence features (an aggregate) with its own annotation. e.g. a single EMBL/GenBank/DDBJ entry

Note: Bioperl is not tied heavily to file formats, however, the above objects do map to file formats sensibly and the examples are given to help bioinformaticians.


By having this split we avoid a lot of nasty circular references (sequence features can hold a reference to a sequence without the sequence holding a reference to the sequence feature). See Bio::PrimarySeq and Bio::SeqFeatureI for more information.

Personal tools
Namespaces
Variants
Actions
Main Links
documentation
community
development
Toolbox