GlimmerHMM¶

Description¶

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. The variable-length feature states (e.g., exons, introns, intergenic regions) are implemented using Nth-order interpolated Markov models (IMM) as described in Delcher et al. 1999 for N=8. Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

Environment Modules¶

Run module spider glimmerhmm to find out what environment modules are available for this application.

Environment Variables¶

HPC_GLIMMERHMM_DIR - installation directory
HPC_GLIMMERHMM_BIN - executable directory
HPC_GLIMMERHMM_DOC - documentation directory
HPC_GLIMMERHMM_TRN - training data directory

Categories¶

biology, annotation