Difference between revisions of "GlimmerHMM"
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(Created page with "Category:SoftwareCategory:BiologyCategory:Microbial Annotation {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|glimmerhmm}} |{{#vardefine:url|http://ccb.jhu.edu...") |
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Annotation]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|glimmerhmm}} | |{{#vardefine:app|glimmerhmm}} | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_TRN - training data directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 17:09, 15 August 2022
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 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)
Environment Modules
Run module spider glimmerhmm to find out what environment modules are available for this application.
System Variables
- HPC_GLIMMERHMM_DIR - installation directory
- HPC_GLIMMERHMM_BIN - executable directory
- HPC_GLIMMERHMM_DOC - documentation directory
- HPC_GLIMMERHMM_TRN - training data directory