Difference between revisions of "GeneMark-ES"

From UFRC
Jump to navigation Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|REPLACE}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTI...")
 
 
(2 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|REPLACE}}
+
|{{#vardefine:app|GeneMark-ES}}
|{{#vardefine:url|REPLACE}}
+
|{{#vardefine:url|http://exon.gatech.edu/}}
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
Line 18: Line 18:
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
GeneMark is documented as the most accurate prokaryotic gene finder. GeneMark.hmm-P and GeneMark.hmm-E programs are predicting genes and intergenic regions in a sequence as a whole. They use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.
+
GeneMark is documented as the most accurate prokaryotic gene finder. GeneMark.hmm-P and GeneMark.hmm-E programs are predicting genes and intergenic regions in a sequence as a whole. They use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions. For more information see Background and Publications.
  
 
<!--Modules-->
 
<!--Modules-->
Line 24: Line 24:
 
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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 16:44, 27 May 2022

Description

GeneMark-ES website  

GeneMark is documented as the most accurate prokaryotic gene finder. GeneMark.hmm-P and GeneMark.hmm-E programs are predicting genes and intergenic regions in a sequence as a whole. They use the Hidden Markov models reflecting the "grammar" of gene organization. The GeneMark.hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions. For more information see Background and Publications.

Environment Modules

Run module spider GeneMark-ES to find out what environment modules are available for this application.

System Variables

  • HPC_GENEMARK-ES_DIR - installation directory