myorfeome to run in linux online

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

Quick description about myorfeome to run in linux online:

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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