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-0.01.tar.gz. Untar and enter the created folder:
tar -xf vBIO-BATI-0.01.tar.gz
cd vBIO-BATI-0.01
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.