Introduction
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:
-
It is slow: Due to the limited memory space reserved
for an applet, the program runs slowly and will run out of memory quickly if
the level is set far above the default of eight.
-
File saving is disabled. Because of this, the color map changes
are session specific and are not saved anywhere. Also, storing frequency
files is disabled.
- There are quirks: The JavaVM varies from browser to browser, so some unpredictable
things may happen. The only known quirk at this time is that some versions of netscape display the
radio button labels incorrectly in the Axes menu until the label itself is clicked on.
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.)
-
humanIe.fna (106 kb, Homo sapiens DNA sequence from PAC 747L4 on
chromosome 1q23-24)
-
yeastI.fna (229 kb, Saccharomyces cerevisiae chromosome I, complete
chromosome sequence)
-
myge.fna (576 kb, Mycoplasma genitalium, complete sequence)
-
myp.fna (809 kb, Mycoplasma pneumoniae M129 complete genome)
-
bb.fna (903 kb, Genomic sequence of a Lyme disease spirochete, Borrelia
burgdorferi)
-
moco.fna (192 kb, Molluscum contagiosum virus subtype 1, complete
genome)
-
mesa.fna (238 kb, Melanoplus sanguinipes entomopoxvirus, complete
genome)
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
NIST ITL
Revised 7/14/2000