SHIFTY Version 1.4 README file ------------------------------ Important --------- If you have already downloaded SHIFTY Version 1.3, then you do not need to download the entire Version 1.4. You can just download the upgrade package shifty-upgrade-v1.4. If you have not already downloaded SHIFTY Version 1.3, or if you have an older version, then you need to download the entire Version 1.4. Purpose ------- This Web-based server is for those interested in rapidly and accurately predicting the 1H, 13C and/or 15N chemical shifts of proteins and peptides using only the protein sequence as input. It uses sequence alignments to previously assigned proteins and a parameterized extrapolation method to predict the chemical shifts of a given query sequence. Included Files and Directories ------------------------------ Once you have unzipped the file with the command "gunzip shifty-v1.x.tar.gz", and untarred the file with the command "tar -xpvf shifty-v1.x.tar" (or combined the two with "gunzip -c shifty-v1.x.tar.gz | tar -xpvf - "), you should have the following directories and files within the shifty directory: - progfiles (directory): - Makefile - makefile for all executable programs (shifty.cgi, append, helpfile.cgi) - VERSION - version of program - align.c - code for aligning query and database sequences - append.c - functions that will append NMR STAR entries from BMRB database to shifty databases - calc.c - code for performing calculations - helpfile.c - code for help file - init.c - code for performing initialization - io.c - code for performing input/output operations - main.c - main C code file - misc.c - contains miscellanious functions - print.c - printing and output functions - shifty.h - shifty header file - shifty.parms - shifty parameters file - unix.c - UNIX specific functions - wt.homology - homolpogy scoring matrix - html (directory): - images (directory): contains all images used by HTML files. - cgi-bin(directory): contains all files that will be used by CGI programs. - shifty.html - main HTML file. - append (directory) : This directory will contain the append program when installation has been finished. - README - this readme file Installation and Setup ---------------------- To setup the executable and CGI programs, simply go into the progfiles directory and type "make". This will make the shifty.cgi and helpfile.cgi files and move them into the cgi-bin in the html directory. It will also make the append program which will then be moved into the append directory. To make any of these programs seperately, simply type make followed by the name of the executable file (e.g. make shifty.cgi). Now, unless you would like to edit or play around with the source code, you are done with the progfiles directory. All you need to do is move the whole html directory (and everything in it) on to your web server with a command like "mv html ~/yourwebserver" Now the main access point for the shifty program is the shifty.html file, which you can locate with your web browser (Note that you may have to change the access permissions). To use the append program, simply go into the append directory and execute it whenever you would like to append entries to the existing databases. Program Descriptions -------------------- shifty.cgi - This is the main CGI program that can ONLY be accessed from the shifty.html file. The HTML file contains a form based submission which takes in the input sequence, the shift type, and the top number of matches wanted, and then executes shifty.cgi and displays the output on your internet browser. helpfile.cgi - This CGI script totals the number of entries in each of the databases and arranges the titles of the entries into separate files. It also displays a help page to the browser. This program can also only be accessed from the shifty.html file. append - The append program allows you to append new entries in the BioMagResBank's NMR STAR format (any bmrXXXX.str file) to the SHIFTY databases. The program translates the NMR-STAR format to the SHIFTY format and also extracts information such as the name, the authors, and the accession number, and adds this information to the databases as well. Trobleshooting -------------- Q. I get a message like "500 Server Error" whenever I try to access the help file or the shifty program from the shifty.html web page, why? A. You may have compiled the programs on a different machine than the one you are running it on. You can only run the CGI programs from the same machine it was compiled on, so if it was compiled on a Sun, then you must put the programs on the Sun's web server. Q. I get a message like "500 Server Error" only when I try to access the help file, but everything works fine when I access the shifty program. Why? A. There may be something wrong with the access permissions that the help file needs. If you untarred the shifty-v1.3.tar file with the command "tar -xvf shifty-v1.3.tar" instead of "tar -xpvf shifty-v1.3.tar", then the access permissions were not saved, and you can either set them again or you can delete everything and start over. (To reset the permissions, simply change directories into the html/cgi-bin directory and type chmod go=rw *titles). Q. Whenever I try to run either the help file or shifty program, I get the message "Method "POST" not allowed", why? A. It could be that your web server has not been configured properly. If you are using a Linux or Open BSD type system, then this could be the case. This message should not appear if you are using a Sun or a SGI. Supported Platforms ------------------- The SHIFTY programs have been compiled and tested on various Sun OS and SGI machines, but never on a Linux or Open BSD type system. Therefore, the performance of the programs on the Linux or Open BSD type systems is undefined. Authors ------- Authors: David Wishart, M. Scott Watson, Robert Boyko, Brian Sykes, Anuj Ranjan Funding for this project has been provided by the Medical Research Council of Canada , Bristol-Myers Squibb(Canada), Alberta heritage Fund for Medical Research, and the Protein Engineering Networks of Centres of Excellence (Canada). ---------------------------------------------------------------------------- Last updated April 29, 1999 by Anuj Ranjan - anuj@cs.ualberta.ca