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

See All Activity >

Categories

Bio-Informatics

License

BSD License

Follow MyOrfeome

MyOrfeome Web Site

Other Useful Business Software
Our Free Plans just got better! | Auth0 Icon
Our Free Plans just got better! | Auth0

With up to 25k MAUs and unlimited Okta connections, our Free Plan lets you focus on what you do best—building great apps.

You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
Try free now
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of MyOrfeome!

Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Unix Shell, Perl

Database Environment

MySQL

Related Categories

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

Registered

2009-08-25