EnglishFrenchSpanish

Ad


OnWorks favicon

MyOrfeome

Free download MyOrfeome Linux app to run online in Ubuntu online, Fedora online or Debian online

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.

Download and run online this app named MyOrfeome with OnWorks for free.

Follow these instructions in order to run this app:

- 1. Downloaded this application in your PC.

- 2. Enter in our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 3. Upload this application in such filemanager.

- 4. Start the OnWorks Linux online or Windows online emulator or MACOS online emulator from this website.

- 5. From the OnWorks Linux OS you have just started, goto our file manager https://www.onworks.net/myfiles.php?username=XXXXX with the username that you want.

- 6. Download the application, install it and run it.

MyOrfeome


Ad


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.
  • ____________________________________________________________________
  • 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

Bio-Informatics

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.


Ad