MyOrfeome Files

MyOrfeome 2009-2011 Bugs: email me at jdmendez (at) infomedicint.com


Requires:

Ubuntu 10.04 (Lucid)
perl
ncbi-blast 2.2.25
MySQL 5 or higher
Linux tools (cat, awk)

Installation

1. Untar the program.

Go to any folder where you want the script to reside.

$untar -xf MyOrfeome-beta-1_1.tar

2. Go to the script directory where you install it (cd myorfeome)

3. Configure enviromental variables on file `myorfeome`

$vi myorfeome

-If you dont have BLAST on the enviromental PATH variable,
then you can add it here.

-Change the database password. Warning, the password you use will be available through the
enviromenal variables.


Running

1. Inside the script directory, create your working directory
mkdir project1

2. Copy your query fasta file and the database in fasta format on your working directory.
(in this version, both have to be previously translated)

$ cp MyProteome.fasta project1/
$ cp ProteinDatabase.fasta project1/


2. In the script directory, run the script and complete the questions.

$./myorfeome

When ask to provide the working directory, provide the absolute path.


3. When done, you results will be in tabular format in a text file on the working directory.
The name of the file is a numeric prefix that represent the time you ran it.