University of Hamburg - to research, to teach, to educate and form, to homepage
ZBH
ZBHCenter for Bioinformatics

Photo: UHH/Denstorf

LTRharvest

is an efficient and flexible software for de novo detection of LTR retrotransposons.

Features

LTRharvest computes boundary positions of potential LTR retrotransposons in genomic target sequences.
The program allows for fast computation of large data sets, e.g. complete vertebrate genomes on the order of 2–3 gigabases. The program accepts sequences in multiple FASTA format (plain or gzipped) and is therefore able to work on whole genome shotgun (WGS) sequencing data, which usually come as multiple unordered contigs.
For the prediction, LTRharvest implements several filters, like LTR length and distance, TSD length and motifs. Since LTR retrotransposon features are mostly species specific, every filter can be switched on or off and is free for parameterisation.
The program reports predictions in tabular fashion and/or in GFF3 format suitable for further processing, for example using LTRdigest. The predicted LTR retrotransposon sequences are reported in FASTA format.
LTRharvest is an open source software that can easily be modified and extended to satisfy further needs.
For a detailed description of the software see the manual. An independent source of information can be found in the blog of Avril Coghlan.

Availability

The source code is freely available as part of GenomeTools which is released under a BSD-like open source license. Please get the latest stable source or binary distribution from the GenomeTools web site.

LTRharvest is also currently available in the Debian unstable and Ubuntu raring and saucy package repositories (genometools package) as part of Debian Med.

Test data sets and Python scripts used for the comparison of LTRharvest predictions to the reference annotations of S. cerevisiae and D. melanogaster can be found here.

Developers

David Ellinghaus, d.ellinghaus(at)ikmb.uni-kiel.de
Sascha Steinbiss, steinbiss(at)zbh.uni-hamburg.de
Stefan Kurtz, kurtz(at)zbh.uni-hamburg.de
Ute Willhoeft, willhoeft(at)zbh.uni-hamburg.de

Publication

D. Ellinghaus, S. Kurtz, and U. Willhoeft:
LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
BMC Bioinformatics, 9:18 (2008)

Contact

Ute Willhoeft, Stefan Kurtz
Center for Bioinformatics, University of Hamburg
Bundesstr. 43, 20146 Hamburg, Germany
Phone +49 40 42838 7316, Fax. +49 40 42838 7312