OrthoMCL

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Category

Bioinformatics

Program On

zcluster

Version

2.0.9

Author / Distributor

More details is at OrthoMcl

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."

More details is at OrthoMcl

Running Program

Also refer to Running Jobs on zcluster /usr/local/orthomcl/latest points to the latest version at /usr/local/orthomcl/2.0.9

OrthoMCL uses mysql as backend database, contact us about mysql information before use this app. And email us once job is done. Database will be removed upon user's notification. There is limited resource to support mysql applications at GACRC, permission granted by case and resource.

Example of a shell script sub.sh to run on at the batch queue:

#!/bin/bash
cd working_directory
/usr/local/orthomcl/latest/bin/orthomclInstallSchema orthomcl.config
time /usr/local/orthomcl/latest/bin/orthomclLoadBlast orthomcl.config similarSequences.txt

Sample of configure file is at /usr/local/orthomcl/latest/config/orthomcl.gacrc.config

Example to submit to the queue

qsub  -q queueName sub.sh

Documentation

for more extensive options. More details is at OrthoMcl

/usr/local/orthomcl/latest/bin/orthomclInstallSchema

Create OrthoMCL schema in an Oracle or Mysql database.

usage: orthomclInstallSchema config_file sql_log_file table_suffix

where:
  config_file : see below
  sql_log_file : optional log of sql executed
  table_suffix : optional string to append to database object names

EXAMPLE: orthomclSoftware/bin/orthomclInstallSchema my_orthomcl_dir/orthomcl.config my_orthomcl_dir/install_schema.log

NOTE: the database login in the config file must have the required database privileges on the tables specified in the config file.

Sample Config File:

dbVendor=oracle  (or mysql)
dbConnectString=dbi:Oracle:orthomcl
dbLogin=my_db_login
dbPassword=my_db_password
oracleIndexTablespace=
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch

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/usr/local/orthomcl/latest/bin/orthomclLoadBlast --help
Load Blast results into an Oracle or Mysql database.

usage: orthomclLoadBlast config_file similar_seqs_file

where:
  config_file :       see below
  similar_seqs_file : output from orthomclParseBlast 

EXAMPLE: orthomclSoftware/bin/orthomclLoadBlast my_orthomcl_dir/orthomcl.config my_orthomcl_dir/similarSequences.txt

NOTE: the database login in the config file must have update/insert/truncate privileges on the tables specified in the config file.

Sample Config File:

dbVendor=oracle  (or mysql)
dbConnectString=dbi:Oracle:orthomcl
dbLogin=my_db_login
dbPassword=my_db_password
similarSequencesTable=SimilarSequences

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Installation

Source code downloaded from OrthoMcl

System

64-bit Linux