Module:Bio::DB::GFF

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Bio::DB::GFF
PDoc Bio::DB::GFF
CPAN Bio::DB::GFF
metaCPAN Bio::DB::GFF


Introduction

The Bio::DB::GFF Perl module is an interface to a database of simple sequence feature annotations and sequence data. For efficiency, features and sequences are stored in a relational database. Data is expected to be loaded from a GFF or GFF3 format file. The module and its dependencies serve as the basis for data access in GBrowse and is DAS compliant.

The relational database is optimized for positional queries allowing a variety of data mining operations, such as:

  • finding sequence features that are within a certain distance of each other
  • finding sequence features that overlap.

The module can also store large contiguous sequences and extract sub-sequences rapidly.

See also: Bio::DB::GFF::RelSegment, Bio::DB::GFF::Feature, and Bio::DB::GFF::Adaptor::dbi.

Related modules

Bio::DB::SeqFeature.

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