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GlimmerHMM |
Overview
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).
System requirements
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.
Accuracy
GlimmerHMM has been trained on several species including Arabidopsis thaliana, Coccidioides species, Cryptococcus neoformans, and Brugia malayi.
| Nuc Sens | Nuc Spec | Nuc Accur | Exon Sens | Exon Spec | Exact Genes | Size of test set | |
| Arabidopsis | 97% | 99% | 98% | 84% | 89% | 60% | 809 genes |
| Cryptococcus | 96% | 99% | 98% | 86% | 88% | 53% | 350 genes |
| Coccidioides | 99% | 99% | 99% | 84% | 86% | 60% | 503 genes |
| Brugia | 93% | 98% | 95% | 78% | 83% | 25% | 477 genes |
Obtaining GlimmerHMM
This software is OSI
Certified Open Source Software .
To download the complete GlimmerHMM system, just click here .
After downloading, uncompress the distribution file by typing:% tar -xzf GlimmerHMM.tar.gz
A directory named 'GlimmerHMM/' will be created which contains the executable, training data sets, and other supporting files.
Contact Information
Please consult the current GlimmerHMM page for contact information.
References
1. W.H. Majoros, M. Pertea, and S.L. Salzberg.
TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders (73K, PDF format)
Acknowledgements
The development of GlimmerHMM was supported by the NIH under grants R01-LM06845 and R01-LM007938.