Genoman

Genoman (short for genome analysis) is an object-oriented Perl library for accessing and manipulating genome annotation data (e.g. genomic locations of genes and other features, alignments of transcript sequences to a genome, and alignments between different genomes). Genoman defines a set of classes for representing such data. The classes are designed to be flexible and sufficiently efficient to allow their use in analysis pipelines for dealing with large data sets. The library is designed to allow data retrieval from different types of files and databases in a consistent manner, into objects of the same classes. Genoman can be supplemented with custom-written database interface classes for accessing particular databases. The current version of Genoman includes an interface for retrieving data from the UCSC Genome Browser database. Interfaces for accessing other databases may be added to Genoman in the future, depending on the needs of the developers.

To download the package, execute the following subversion command in your shell:

svn co http://www.ii.uib.no/svn/lenhard/genoman/

(For this to work, subversion must be installed on on your system.)

You can also browse the subversion repository.

Before using Genoman, please read the README file.

To learn how to use it, you may want to have a look at:


Genoman is Copyright (C) 2008 by Pär Engström. It is free software; you can redistribute it and/or modify it under the same terms as Perl itself (see http://dev.perl.org/licenses/).