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Disclaimer for mGene 0.1.0 beta

Dear mGene User,

This is the first public release of mGene version 0.1 beta. This software is the result of further development of mGene as described in [1] and is similar to the implementation used for mGene.web described in [2].

The main focus of the improvements relative to [1] is to make it easier to use, the software more stable and applicable to a broad range of organisms. The current version of mGene does not support:

  1. use of whole genome alignments (features used in mGene.multi in [1])
  2. use of alignments of ESTs, cDNAs or proteins (features used in mGene.seq in [1])
  3. Trans-splicing, operons and polyA sites. These feature are primarily important for nematode genomes and are often not necessary for other organisms.
  4. Model selection: All models are trained with preset hyper-parameters. Model-selection can significantly improve the results of the predictions.
  5. Prediction tuning: There are several ways to trade-off sensitivity with specificity in gene prediction. However, right now these expert options are not supported in this version.

There are some additional limitations in this release:

  1. Currently, we implemented some inherent settings for sub-sampling examples to reduce the computation time. Enabling the use of all examples (as in [1]) leads to better results.
  2. Reading genes for training from GFF3 files is tricky. We only accept a gene's annotation, if it satisfies certain, quite stringent conditions, leading to smaller sets for training. In some cases we try to infer missing information, like the open reading frame (which can easily be wrong). Training on poor-quality input data generally leads to a poor prediction performance.
  3. Currently, intermediate files a relatively big and can easily addup to a few gigabytes for a genome like the one of C. elegans. Moreover, depending on the length of the chromosomes/contigs mGene may need considerable amounts of main memory.
  4. Currently, mGene uses regions around annotated genes for training the gene predictor, where we use some heuristic to determine where to cut intergenic regions. (These regions are assembled into blocks for training.) This strategies always works to a certain extend (even for missing genes in the annotation), but is inferior to using fully annotated regions (as done in [1]). There will be more options to control this behaviour in future versions.
  5. Right now we use two versions of the shogun toolbox, leading to problems running the monolithic workflows in octave. This will be solved in the next release.

We are working towards solving these issues, to make the software more stable and to include more features into mGene.

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](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)
[2]Schweikert et al. mGene.web: a web service for accurate computational gene finding. Nucleic Acids Research 2009. (accepted)
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