Module:Bio::DB::GFF

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Pdoc documentation: Bio::DB::GFF CPAN documentation: Bio::DB::GFF

Introduction

Lincoln Stein's interface to a relational database representation of simple feature and sequence data. The data is expected to be loaded from a GFF format file. The system is DAS compliant as well. This module (and its dependencies) serves as the basis for data access of Gbrowse as well.

The module takes a set of sequence features stored in GFF format and loads them into a relational database optimized for positional queries. This allows a variety of data mining operations, such as finding sequence features that are within a certain distance of each other or which overlap. The module can also store large contiguous sequences and extract subsequences rapidly.

Also see Bio::DB::GFF::RelSegment, Bio::DB::GFF::Feature, and Bio::DB::GFF::Adaptor::dbi.

The next incarnation of this system for explicit support of GFF3 is available in this module (and dependancies) Bio::DB::SeqFeature.

Retrieved from "http://www.bioperl.org/wiki/Module:Bio::DB::GFF"
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