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MyOrfeome

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Description

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.

MyOrfeome Web Site

Categories

Bio-Informatics

License

BSD License

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.

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Additional Project Details

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Unix Shell, Perl

Registered

2009-08-25

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