myorfeome

We have hosted the application myorfeome in order to run this application in our online workstations with Wine or directly.

Quick description about myorfeome:

Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way.

It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.

Features:

• Version 2.1: Check for NCBI BLAST somewhere in the path before running.
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• Written in bash, perl
• Can run in linux, Mac OS, or Cygwin environment (Windows).
• Uses MySQL database to generate tables.
• Open Source, under the BSD Licence
• Writen for comparative Poxvirus genomics, but can me adapted for other species.
• Required Software: Pearl, Mysql, Linux, BLAST.
• Future version: generate Feature table for Genbank submission
• Visit our website for latest version.
• Version 2.0: Several bugs corrected. The script copies the default proteome sujects into your working directory. Creates the working directory and verify that your input fasta files exists. Known bugs: fasta files descriptor should not contain special characters such as: !@#$%^&*()_
• Version 1.2 - New things in this version: - Some bugs fixed. - Create output folder automatically. - Check for DB user and password. - Add some comments when running the script. - MOCV proteome included.
• Known bugs: Mysql in Cygwin does not find files. Does not check if fasta files contains only protein seq.

Audience: Science/Research.
User interface: Command-line.
Programming Language: Unix Shell, Perl.
Database Environment: MySQL.

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