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
http://mgene.org/download).  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 http://mgene.org/download or visit our
Galaxy-based webserver at http://mgene.org/web.
 
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
(support@mgene.org or Gunnar.Raetsch@tuebingen.mpg.de). We would be
glad to assist you to obtain the optimal results using mGene.


**The mGene Development Team**


References:

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

