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Bio::Coordinate(3pm) User Contributed Perl Documentation Bio::Coordinate(3pm)


Bio::Coordinate - Modules for working with biological coordinates


version 1.007001


  # create Bio::Coordinate::Pairs or other Bio::Coordinate::MapperIs somehow
  $pair1; $pair2;
  # add them into a Collection
  $collection = Bio::Coordinate::Collection->new;
  # create a position and map it
  $pos = Bio::Location::Simple->new (-start => 5, -end => 9 );
  $res = $collection->map($pos);
  $res->match->start == 1;
  $res->match->end == 5;
  # if mapping is many to one (*>1) or many-to-many (*>*)
  # you have to give seq_id not get unrelevant entries
  $pos = Bio::Location::Simple->new
      (-start => 5, -end => 9 -seq_id=>'clone1');


Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.


Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


Heikki Lehvaslaiho <>


This software is copyright (c) by Heikki Lehvaslaiho.

This software is available under the same terms as the perl 5 programming language system itself.

2020-11-24 perl v5.32.0