GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
GlimmerHMM is released as source code and was tested on Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any Unix system.
GlimmerHMM has been trained on several species including Arabidopsis thaliana, Coccidioides species, Cryptococcus neoformans, and Brugia malayi.
This software is OSI
Certified Open Source Software .
% tar -xzf GlimmerHMM.tar.gz
A directory named 'GlimmerHMM/' will be created which contains the executable, training data sets, and other supporting files.
Please consult the current GlimmerHMM page for contact information.
1. W.H. Majoros, M. Pertea, and S.L. Salzberg.
TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders (73K, PDF format)