This is the Linux app named MyOrfeome whose latest release can be downloaded as myorfeome-v2.1.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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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.
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
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/myorfeome/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.