Ltrdigest

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Description

Software tool for identification and annotation of characteristic sequence features of LTR retrotransposons in predicted candidates. In particular, LTRdigest can be used to find protein domains, polypurine tracts and primer binding sites.

License

http://genometools.org/license.html

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 ltrdigest and load default version of ltrdigest as

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


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

module avail ltrdigest

and choose explicit version you want to use.

Documentation

http://www.zbh.uni-hamburg.de/fileadmin/gi/LTRdigest/ltrdigestman.pdf

Homepage

http://www.zbh.uni-hamburg.de/?id=207