Lincoln D. Stein > GBrowse > Bio::DB::GFF::Aggregator::match_gap

Download:
GBrowse-2.54.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  5
Open  1
View/Report Bugs
Source   Latest Release: GBrowse-2.55

NAME ^

Bio::DB::GFF::Aggregator::match_gap -- GFF3 match aggregator

SYNOPSIS ^

 -------------------------------------------------
 Aggregator method: match_gap
 Main method:       match
 Sub methods:       match
 -------------------------------------------------

DESCRIPTION ^

This aggregator is used for GFF3 style gapped alignments, in which there is a single feature of method 'match' with a 'Gap' attribute.

The 'Gap' attribute's format consists of a series of (operartion,length) pairs separated by space characters, for example: 'M8 D3 M6'. (see GFF reference for complete explanation)

This module only recognizes the M and D operators, which should be sufficient for simple nucleotide to nucleotide alignments.

################################################################################

BUGS ^

None reported.

SEE ALSO ^

Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR ^

Dmitri Bichko

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

syntax highlighting: