Content-type: text/html Downloads and Documentation

Welcome to the downloads page. Here, you can download several scripts which helped us with our annotations.

In development: You can download a package with tbex, bgmix, bsniffer and genetuner here. This can be installed automatically in *NIX systems:

  • If you have not done so, install blast2:
  • apt-get install blast2
  • Download vBIO-BATI-0.02.tar.gz. Untar and enter the created folder:
  • tar -xf vBIO-BATI-0.02.tar.gz
    cd vBIO-BATI-0.02
  • Install with cpan. This should take care of prerequisites:
  • cpan .
  • If you get a complaint from cpan, sometimes you can install with force successfully:
  • cpan -f .

Old scripts:

To run these scripts, you may need to install these elements:

  • A distribution of Perl v5.8.8 or higher. You can download the best distribution for your system at this page.
  • Perl's BioPerl package. You can find instructions at this page.
  • The BLAST package. You can find the version for your system at this page.
    • Make sure that you add the BLAST executable path to you $PATH enviroment variable, so that you can run BLAST commands from any folder.
  • To run GeneTuner in a *NIX system, you will need the Term::Screen module, which can be found at this page.
  • To run GeneTuner in a Win32 system, you will need the Win32::Console module, which can be found at this page.

There is a tutorial with a simple example to get started with these scripts.

These scripts are free software and can be redistributed under the same terms as Perl. THESE TOOLS ARE PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.

To download to your disk, right-click the hyperlink and choose 'Save as' in the menu.

tb

This short script outputs TBLASTN commmands for a project file. See the tutorial for instructions. Download here.

Usage:

perl tb.pl [project_name]

fix_chr

This script fixes a glitch in the Bio::DB::Fasta module of BioPerl which prevents short lines filled with Ns to load. If you run GeneTuner and find all of the exons shifted, this script may help. Download here.

Usage:

perl fix_chr.pl [file_name]

Creates a new file called 'fixed' with the reformatted sequence.

BlastSniffer

This script helps users to locate genes from TBLASTN alignments. Download here.

Usage:

perl bsniffer.pl [--help] [project_name] [file_name]

See the documentation for further information.

GeneTuner

This script helps users to define exon boundaries in genes defined with BlastSniffer.

  • Dowload the *NIX version here.
  • Dowload the Win32 version here.

Usage:

perl genetuner.pl [--help] [project_name] [file_name]

See the documentation for further information.