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Disclaimer for mGene nGASP

Dear mGene User,

This is the public release of mGene as described in [1]. The primary purpose of this release is to allow, to a certain extend, the reproducability of the prediction results on nematode genomes presented in [1]. This source code is mainly provided for studying how we have implemented the ideas presented in [1] and to reproduce parts of our results (e.g. in conjunction with the considerably easier-to-use mGeneToolbox, available for download from We will NOT support this version for applying mGene to other genomes and will not provide bug fixes. If you are interested in a broader application of mGene, please download the current mGene version at or visit our Galaxy-based webserver at

Note that currently this version will require substantial modification to run on other user's computers, as paths and data are not adapted or configurable.

The nGASP version of mGene supports:

  1. Training and Prediction with the ab initio version of mGene (mGene.init in [1])
  2. Use of whole genome alignments (mGene.multi in [1])
  3. Use of alignments of ESTs, cDNAs or proteins (mGene.seq in [1])
  4. All three versions include training and prediction of trans-splicing, operons and polyA sites.
  5. Model selection of hyper-parameters.
  6. Prediction tuning: There are several ways to trade-off between sensitivity and specificity in gene prediction.

If you are interested in using mGene for annotating an organism's genome or for comparing it with other predictions, please let us know ( or We would be glad to assist you to obtain the optimal results using mGene.

The mGene Development Team


[1](1, 2, 3, 4, 5, 6) Schweikert et al. mGene: Accurate Computational Gene Finding with Application to Nematode Genomes. In Genome Research 2009. (under review)
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