GenomeThreader

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Description

GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation.

License

GenomeThreader is available free of charge.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of genomethreader and load default version of genomethreader as

module avail genomethreader/ # list available modules
module load genomethreader   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail genomethreader

and choose explicit version you want to use.

Documentation

http://genomethreader.org/doc/gthmanual.pdf

Homepage

http://genomethreader.org/