GSAP version 1.0.1
Robin Allaby, Sarah Palmer, Jay Moore

Genomic Species Analysis Program
GSAP takes two (possibly very large) FASTA files and searches one against the other sequence by sequence looking for local alignment hits that are top scoring but not identical. For each alignment, priming sites are identified to generate an (optionally nested) primer design for amplifying segments containing SNPs and indels. This is intended (and we use it) for trawling through genomic and/or RNA data sets of pairwise taxa in order to find points of diagnostic divergence.

 

Download

Save this file to your desktop, and unzip the contents (Macs will probably do this automatically). The GSAP folder within contains the GSAP script and some associated files.

 

Installation

The script requires that your computer has Perl installed.  The first line of the script indicates the location of Perl, and may need to be changed to suit your system.  Macs should be OK, as this script was originally created to run on a Mac.  If you use Windows and don't have Perl installed, you can install the 'industry standard' free Windows Perl ActivePerl (go to http://www.activestate.com/store/activeperl), which we believe is robust and safe to install.

 

GSAP also makes use of NCBI BLAST to search the FASTA files.  The Mac version of BLAST is included, but if you use Windows or Linux you will need to replace this.  The easiest way to do this is to download the BLAST program from the NCBI FTP site, and install it in the folder called BLAST within the GSAP folder created above.  Alternatively, if you already have BLAST installed, you could change the GSAP script to point to your BLAST location.

 

Parameters

GSAP searches two FASTA files against each other, so first it needs to know the names of your two files.  These are the only mandatory parameters.

GSAP can carry out reciprocal BLAST searching between your two files (recommended), and needs to be told not to if you don't want it. This parameter is optional.

For the primer design stage, a target length in bp of the final PCR products is required, and also minimum and maximum lengths.  Similarly, minimum and maximum GC content of products are required.  These parameters are optional.  If you do not specify any, the default values will generate primer designs suitable for amplification of even ancient or damaged DNA.

For further information in detail about parameters and how to change the defaults, see the script header in the file gsap_1.0.1.pl.

For quick start, all you need to do is edit the file gsap.ini, and put in the names of your FASTA files.


Running
On Macs, you can edit the file gsap.ini to add the names of your two FASTA files, then double-click the file GSAP.command.
GSAP is also intended to be run from the command line on any platform.  You can put your chosen FASTA filenames and other parameters in the file gsap.ini or you can specify them explicitly on the command line.  Explicit command line values override the defaults in gsap.ini.  See the script header in the file gsap_1.0.1.pl for more information about command line options.



Changes since previous version

None.


Known bugs

None.

