Department of Computer Science
 Rutgers University

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GeneFinder: Ab initio gene finding

Ab initio gene finding or prediction is still an interesting problem. Current gene finder work well but especially predictions of eukaryotic genes have much space for improvement. Based on Anders Krogh's HMMGene our gene finder is used to test ideas to improve the predictions. One idea is to incorporate external data like gene expression to aid the signal and sequence composition driven prediction. The gene finder is implemented in Python using the python bindings of our own free (LGPL) HMM library General Hidden Markov Model library (GHMM).

Publications

Heinig, Matthias. Development of a Pair HMM based Gene Finder for the Paramecium Genome (2005) [details]

Contact: Janne Grunau (grunau@molgen.mpg.de).