The MetagenomeThreader is software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.

Background

The program MetagenomeThreader implements an algorithm based on the work of Lutz Krause [1] to predict genes in sequences of metagenome projects. It uses BLAST hits to compute both a metagenome sequence as well as reading frame specific combined scores which allows the prediction of coding, or more specifically, fractional coding sequences within metagenome sequences. The MetagenomeThreader is available as open source software.

Availability

The source code is freely available under GenomeTools also refered to as the genome analysis system, here. It is released under a BSD-type open source licence. The test data set, the BLAST hits and the hit sequences that were needed to reconstruct and verify the following described results are also part of GenomeTools.

Developers

David Schmitz-Hübsch, dschmitz(at)zbh.uni-hamburg.de
Stefan Kurtz, kurtz(at)zbh.uni-hamburg.de

Test Results

Here

Publication

In progress.

Contact

Stefan Kurtz
Center for Bioinformatics, University of Hamburg
Bundesstr. 43, 20146 Hamburg, Germany
Phone +49 40 42838 7311, Fax. +49 40 42838 7312

Literature

[1] Krause , L.; Diaz, N. N., Bartels, D.; Edwards, R. A.; Pühler, A.; Rohwer, F.; Meyer, F.; Stoye, J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22:e281-e289, 2006.