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.
  • ____________________________________________________________________
  • 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.

Project Activity

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Categories

Bio-Informatics

License

BSD License

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MyOrfeome Web Site

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Perl, Unix Shell

Database Environment

MySQL

Related Categories

Unix Shell Bio-Informatics Software, Perl Bio-Informatics Software

Registered

2009-08-25
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