Difference between revisions of "OrthoMCL"
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|{{#vardefine:app|orthomcl}} | |{{#vardefine:app|orthomcl}} | ||
|{{#vardefine:url|http://orthomcl.org/}} | |{{#vardefine:url|http://orthomcl.org/}} | ||
| − | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | + | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> |
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
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* HPC_ORTHOMCL_CONF - configuration directory. It contains the orthomcl.config file that provides the MySQL connection settings, credentials, and the database structure. | * HPC_ORTHOMCL_CONF - configuration directory. It contains the orthomcl.config file that provides the MySQL connection settings, credentials, and the database structure. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | For a given OrthoMCL version the /apps/orthomcl/VERSION/config/orthomcl.config file provides a template for configuring an OrthoMCL database. Change the database name from 'orthomcl', which is an existing database containing the data from OrthoMCL authors to your own database that has a name with a pattern <code>'project_user_orthomcl'</code in the string <code>dbConnectString=dbi:mysql:'''orthomcl''':10.13.20.209</code>. MySQL server will allow the orthomcl user to create databases with that name pattern. | |
| + | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
Revision as of 20:22, 15 April 2013
Description
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.
Required Modules
Serial
- orthomcl
System Variables
- HPC_{{#uppercase:orthomcl}}_DIR - installation directory
- HPC_ORTHOMCL_BIN - executable directory
- HPC_ORTHOMCL_CONF - configuration directory. It contains the orthomcl.config file that provides the MySQL connection settings, credentials, and the database structure.
How To Run
For a given OrthoMCL version the /apps/orthomcl/VERSION/config/orthomcl.config file provides a template for configuring an OrthoMCL database. Change the database name from 'orthomcl', which is an existing database containing the data from OrthoMCL authors to your own database that has a name with a pattern 'project_user_orthomcl'</code in the string dbConnectString=dbi:mysql:orthomcl:10.13.20.209. MySQL server will allow the orthomcl user to create databases with that name pattern.