Difference between revisions of "OrthoMCL"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
 
(32 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+
[[Category:Software]][[Category:Biology]][[Category:Genomics]]
<!-- ########  Template Configuration ######## -->
+
{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|orthomcl}}
 
|{{#vardefine:app|orthomcl}}
 
|{{#vardefine:url|http://orthomcl.org/}}
 
|{{#vardefine:url|http://orthomcl.org/}}
<!--Compiler and MPI settings - OPTIONAL -->
+
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
|{{#vardefine:exe|}} <!--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-->
Line 26: Line 11:
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
 
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
+
|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
 
|}
 
|}
 
<!-- ########  Template Body ######## -->
 
<!-- ########  Template Body ######## -->
Line 35: Line 20:
 
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.
 
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.
  
==Available versions==
+
<!--Modules-->
* 2.0
+
==Environment Modules==
<!-- -->
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
{{#if: {{#var: mod}}|==Running the application using modules==
+
==System Variables==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_ORTHOMCL_BIN - executable 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.
+
* HPC_ORTHOMCL_CONF - configuration directory. It contains template orthomcl.config files for SQLite and MySQL connection settings, credentials, and database structures.
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+
===Configuration===
 +
;Note
 +
: Only SQLite is supported as an OrthoMCL database out of the box at this time unless you attempt to stand up your own MariaDB database in another job using a container on your own.
 +
 
 +
The '<code>$HPC_ORTHOMCL_CONF/orthomcl.config</code>' file provides a template for configuring an OrthoMCL SQLite database. Copy it to your working directory with
 +
$ cp $HPC_ORTHOMCL_CONF/orthomcl.config .
 +
 
 +
The '<code>$HPC_ORTHOMCL_CONF/orthomcl.config.sql</code>' file provides a template for configuring an OrthoMCL MySQL database. Copy it to your working directory with
 +
$ cp $HPC_ORTHOMCL_CONF/orthomcl.config.sql .
 +
 
 +
Don't forget to create the schema with the following '''before''' creating a database:
 +
orthomclInstallSchema orthomcl.config
 +
 
 +
 
 +
A wrapper script -- '<code>orthomcl_wrapper_SQLITE</code>' -- that creates a suitable orthomcl.config file and automates much of the pipeline is provided:
 +
 +
$ orthomcl_wrapper_SQLITE -p compliantFASTA -u 2 -s 100
 +
-p path to folder with input fasta files
 +
-u position of unique IDs in fasta headers
 +
-s number of parallel blast jobs to run in a slurm array.
 +
 
 +
 
 +
The wrapper script writes a '<code>run_split_blast_array.sh</code>' script that can be modified to resubmit blast jobs if necessary, and a '<code>finish.orthomcl.sh</code>' script to be run after all blast jobs complete.
 +
 
 +
 
 +
* Documentation for SQLite support can be found at https://github.com/stajichlab/OrthoMCL.
 +
 
 +
* OrthoMCL User Guide can be found at [http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0612s35/full Wiley Online Library].
 +
 
 +
* The original publications that describe the functionality of the software are [http://dx.doi.org/10.1101%2Fgr.1224503 10.1101/gr.1224503] and [http://dx.doi.org/10.1093%2Fnar%2Fgkj123 10.1093/nar/gkj123].
 +
 
 +
 
 +
 
 +
|}}
 
{{#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.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
+
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
Line 55: Line 73:
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
+
If you publish research that uses {{#var: app}} you have to cite it as follows:
WRITE CITATION HERE
+
#Feng Chen, Aaron J. Mackey, Christian J. Stoeckert, Jr., and David S. Roos. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006 34: D363-8. '''Please cite this paper if you publish research results benefited from OrthoMCL-DB.'''
 +
#Li Li, Christian J. Stoeckert, Jr., and David S. Roos.  OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003 13: 2178-2189.
 +
#Feng Chen, Aaron J. Mackey, Jeroen K. Vermunt, and David S. Roos. Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes. PLoS ONE 2007 2(4): e383.
 
|}}
 
|}}

Latest revision as of 22:40, 28 January 2024

Description

orthomcl website  

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.

Environment Modules

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

System Variables

  • HPC_ORTHOMCL_DIR - installation directory
  • HPC_ORTHOMCL_BIN - executable directory
  • HPC_ORTHOMCL_CONF - configuration directory. It contains template orthomcl.config files for SQLite and MySQL connection settings, credentials, and database structures.

How To Run

Configuration

Note
Only SQLite is supported as an OrthoMCL database out of the box at this time unless you attempt to stand up your own MariaDB database in another job using a container on your own.

The '$HPC_ORTHOMCL_CONF/orthomcl.config' file provides a template for configuring an OrthoMCL SQLite database. Copy it to your working directory with

$ cp $HPC_ORTHOMCL_CONF/orthomcl.config .

The '$HPC_ORTHOMCL_CONF/orthomcl.config.sql' file provides a template for configuring an OrthoMCL MySQL database. Copy it to your working directory with

$ cp $HPC_ORTHOMCL_CONF/orthomcl.config.sql .

Don't forget to create the schema with the following before creating a database:

orthomclInstallSchema orthomcl.config


A wrapper script -- 'orthomcl_wrapper_SQLITE' -- that creates a suitable orthomcl.config file and automates much of the pipeline is provided:

$ orthomcl_wrapper_SQLITE -p compliantFASTA -u 2 -s 100
-p path to folder with input fasta files 
-u position of unique IDs in fasta headers
-s number of parallel blast jobs to run in a slurm array.


The wrapper script writes a 'run_split_blast_array.sh' script that can be modified to resubmit blast jobs if necessary, and a 'finish.orthomcl.sh' script to be run after all blast jobs complete.




Citation

If you publish research that uses orthomcl you have to cite it as follows:

  1. Feng Chen, Aaron J. Mackey, Christian J. Stoeckert, Jr., and David S. Roos. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006 34: D363-8. Please cite this paper if you publish research results benefited from OrthoMCL-DB.
  2. Li Li, Christian J. Stoeckert, Jr., and David S. Roos. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003 13: 2178-2189.
  3. Feng Chen, Aaron J. Mackey, Jeroen K. Vermunt, and David S. Roos. Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes. PLoS ONE 2007 2(4): e383.