OrthoMCL

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences

User Guide

OrthoMCL uses a database to run its analyses. If you would like to use OrthoMCL on our servers, please send us an email and we’ll set up access to our database server for you.

After your database account is setup, you can configure OrthoMCL with a orthomcl.config file like this:

dbVendor=mysql 
dbConnectString=dbi:mysql:your_username:data-orthomcl.ibest.uidaho.edu:3306
dbLogin=your_username
dbPassword=the_password_we_give_you
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5

Once you have that set up, you can initialize the database using:

module load orthomcl
orthomclInstallSchema orthomcl.config

You can connect to your orthomcl database with:

mysql -u your_username -p --host=data-orthomcl.ibest.uidaho.edu -D your_username

You will then be prompted for your password

You can clear tables from your database by connecting, then running the DROP TABLE command. Use caution, as there is no way to recover a dropped table.

ibestadm@fortytwo ~ $ mysql -u ibestadm -p --host=data-orthomcl.ibest.uidaho.edu -D ibestadm
Enter password: 
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 30
Server version: 5.1.73 Source distribution

Copyright (c) 2000, 2013, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> show tables
    -> ;
+--------------------+
| Tables_in_ibestadm |
+--------------------+
| CoOrtholog         |
| InParalog          |
| InterTaxonMatch    |
| Ortholog           |
| SimilarSequences   |
+--------------------+
5 rows in set (0.01 sec)

mysql> drop table CoOrtholog;
Query OK, 0 rows affected (0.00 sec)

You can also connect to the database using a graphical client like SequelPro (Mac, free).

After you drop a table rerun the orthomclInstallSchema orthomcl.config command.

BLAST all v all

module load ncbi-blast
makeblastdb -in goodProteins.fasta -dbtype prot -out goodProteinsBLAST.db