OrthoMCL_notes

Notes on how to use OrthoMCL. These notes were generated while following the UserGuide.

Installation

We'll need the following.

NCBI BlastP
perl, test for presence with
$ perl --version
MySQL, test for presence as follows.
$ mysql --version Use apt-get install if not present.
mcl, test for presence as follows. $ mcl --version Use apt-get install if not present.
OrthoMCL, download tarball from the site.

MySQL notes

Start and stop the server.

$ sudo service mysql status
$ sudo service mysql start
$ sudo service mysql stop

Common commands.

 mysql --user=root --password=the_mysql_root_password
 SHOW DATABASES;
 CREATE DATABASE orthomcl;
 SHOW TABLES FROM music;
 USE music;
 SHOW TABLES;
 EXIT;
 QUIT;

OrthoMCL uses a database named orthomcl which makes it a good example for the CREATE command.

Determine MySQL port number.

SHOW VARIABLES WHERE Variable_name = 'port';

The default is 3306 and is known to most of the internet, which is a security issue. This can be changed by editing my.cnf (for me it was /etc/mysql/my.cnf) to change the port parameter. Then stop and sart your mysql server.

Configuration

Add to your bash PATH.

export PATH=~/bin/orthomclSoftware-v2.0.9/bin:$PATH

Create my_orthomcl_dir.
Copy orthomclSoftware/doc/Main/OrthoMCLEngine/orthomcl.config.template to my_orthomcl_dir/orthomcl.config.
Edit this file as directed in the UserGuide.txt.

Install perl's DBI module.

sudo apt-get install libdbi-perl
sudo apt-get install libdbd-mysql-perl

Run the orthmclInstallSchema program to install the schema. (Run the program with no arguments to get help. This is true of all following orthomcl programs.)

FASTA sanitization

We'll need to make our FASTA files OrthoMCL compliant.

mkdir compliantFasta/
cd compliantFasta/
orthomclAdjustFasta pinf ../pinf_omcl.fasta 2
orthomclAdjustFasta pram ../pram_omcl.fasta 1
orthomclAdjustFasta psoj ../psoj_omcl.fasta 1
cd ..

We then filter the genes based on length and percent stop codons.

orthomclFilterFasta compliantFasta/ 10 20

blastp

First we need to make our blast database.

~/bin/ncbi-blast-2.7.1+/bin/makeblastdb -in goodProteins.fasta -dbtype prot

Then perform the search. Note that the UserGuide states we need to use -m 8. This option does not exist in the current version of blastP 2.7.1+. Instead, we've used -outfmt 6. This should be a tab delimited file containing the following columns (m 8): query_name, hitname, pcid, len, mismatches, ngaps, start('query'), end('query'), start('hit'), end('hit'), evalue, bits

~/bin/ncbi-blast-2.7.1+/bin/blastp -query goodProteins.fasta -db goodProteins.fasta -outfmt 6 -evalue 1e-5 -out myBlastP.out

orthomclBlastParser

mkdir my_orthomcl_dir
orthomclBlastParser myBlastP.out compliantFasta/ >> my_orthomcl_dir/similarSequences.txt

orthomclLoadBlast

orthomclLoadBlast config_file my_orthomcl_dir/similarSequences.txt

Where config_file is as follows

dbVendor=mysql
dbConnectString=dbi:mysql:orthomcl
dbLogin=root
dbPassword=myPassword
similarSequencesTable=SimilarSequences

orthomclPairs

orthomclPairs config_file2 pairslog cleanup=no

Where config_file2 appears below.

dbVendor=mysql
dbConnectString=dbi:mysql:orthomcl
dbLogin=root
dbPassword=my_db_password
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5

orthomclDumpPairsFiles

Here we can reuse the config file from orthomclPairs.

orthomclDumpPairsFiles config_file2

This should create a directory called pairs/.

mcl

mcl mclInput --abc -I 1.5 -o my_orthomcl_dir/mclOutput

orthomclMclToGroups

orthomclMclToGroups my_prefix 1000 < mclOutput > groups.txt

You're finished!

knausb/OrthoMCL_notes