GenPatterns is a computer program developed by Fern Hunt, Antti Pesonen, and Dan Cardy of the National Institute of Standards and Technology. It can be used to analyze and visualize patterns in DNA sequencies. Subsequence frequency visualization is based on a two dimensional histogram developed by Bailin Hao [Hao B. et al, A Combinatorial Problem Related to Avoided and Under-Represented Strings in Bacterial Complete Genomes. Proc. of Combinatorics and Physics, Los Alamos, August 1998]. In addition there are other analytical and visual tools such as sequence modeling tools, gap plots, and DNA walks. The program is available as a Java applet here for demonstration purposes. Since the program (and the applet) is written in Java, it can be run on most mainstream operating systems.

Help is available on the following topics: The complete User's Guide is available online (html) and in Word document format (750 KB)).

Running the program

The applet version of GenPatterns is a demonstration of the "stand alone", GenPatterns program. The applet version has some restrictions: To avoid the above limitations, download the full version by clicking here.
The following DNA example data are available: (Any FASTA file can be used with the full version.) Directions:
When the program asks to enter an input file name, enter one of the names above. Only these data files can be used because applet enabled web browsers have security restrictions that limit access to local resources (like files). There is a way to relax these restrictions, but the current approach was selected for simplicity. Keep in mind that the "stand alone" version of GenPatterns does not have these limitations.
Start the GenPatterns applet by clicking the button below.

Original code by Antti Pesonen
Update to Version 1.6 by Dan Cardy
Project Supervisor: Dr. Fern Hunt
Revised 7/14/2000