This page contains a collection of Perl scripts I made to automate submitting queries to the various protein structure prediction programs described on the main page (Thanks to Nathan Patwardhan for helping me on this). These scripts require Perl 5.005_03 or newer with the LWP module (libwww-perl5) installed. To run a script, download the files using the links below and type “perl scriptname.pl” at the command prompt to run each script.
blastscript.pl – Script for Blast search using the NPSA site
ssscript.pl – Script for Secondary Structure prediction consensus using the NPSA site
123Dscript.pl - Script for the 123D+ threading program
gtscript.pl – Script for the GenTHREADER threading program
pstrings.txt – Sample file containing protein strings
These scripts are currently hardcoded to generate a file named “output.htm” as output. Eventually this will be changed and the output will be exported into an SQL database(see Main Page for more details). The scripts are also currently hardcoded to read the protein strings from a file named “pstrings.txt”. A sample of this file may be downloaded from the above link. This sample file contains protein strings for: Mammalian Serine Racemase, Bacterial Serine Racemase and L-Lysine 2,3-Aminomutase (in that order).
Click here to view a design prototype for a program that automatically generates scripts similar to those above, given a web-based query form.