Copyright: Copyright (c) by Jason H. Moore


Fractal DNA Imager Help

General Information

About Fractal DNA Imager 1.0

About the Author and Software Visions

Technical Support and User Feedback

Registering Fractal DNA Imager

Copyright Notice

How to Use Fractal DNA Imager

Overview

Working With DNA Sequences

Imaging DNA sequences

Suggested Reading

Selected Papers


About Fractal DNA Imager 1.0

Fractal DNA Imager

Version 1.0 SHAREWARE

Copyright (c) 1994 by Jason H. Moore

ALL RIGHTS RESERVED

UNREGISTERED 30-DAY TRIAL COPY


About the Author
About the Author and Software Visions

Jason H. Moore received his B.S. in Biological Sciences from Florida State University and his M.S. in Human Genetics from the University of Michigan Medical School.  He is currently working on a M.A. in Statistics and a Ph.D. in Human Genetics at the University of Michigan in Ann Arbor.  His interests include statistical, computational and molecular genetics as well as complexity theory and artificial intelligence.

Jason founded Software Visions with the goal of writing and distributing user-friendly scientific software for education and research.  Fractal DNA Imager is the first in a series of Windows programs with a computational genetics and complexity theme.  Several genetic algorithm-based Windows programs are under development and are next in line for distribution.


Technical Support and User Feedback

Technical support is available for registered users via e-mail or regular mail.

e-mail:	jhm@superh.hg.med.umich.edu  (University of Michigan)

jasonUMICH@aol.com  (America Online)

mail:	Jason H. Moore,

Software Visions,

615 Hidden Valley Drive, #211,

Ann Arbor, MI  48104

This is the first version of Fractal DNA Imager and there are bound to be several bugs.  If you find any bugs or have any suggestions, ideas or impovements for the program please send your reports to one of the addresses above.  In addition, I would love to hear about how you are using this program either in an educational or research setting.  If enough user feedback is received I will consider sending out a newsletter informing registered users of Fractal DNA Imager applications and research findings.  Ideas for Windows programs that you would like to see or think would be useful are certainly welcome.


Registering Fractal DNA Imager

Fractal DNA Imager 1.0 is shareware.  The author grants permission for you to use this software on a trial basis for a time period not to exceed 30 days.  If you decide to use Fractal DNA Imager for longer than 30 days, registration is required.  The benefits to registration are:

1)  Technical support.

2)  Free upgrades.

3)  You will be added to the Software Visions mailing list.

4)  You will be supporting the improvement of Fractal DNA Imager as well as the

      development of other software packages.

The registration fee is $20.00 (US dollars) per computer.  Information on obtaining a site-license for multiple computers or a network is available upon request.  Make checks payable to Jason H. Moore.

Please send registration fees to:	Jason H. Moore,

Software Visions,

615 Hidden Valley Dr., #211,

Ann Arbor, MI  48104

THIS SOFTWARE IS PROVIDED AS IS.  THERE ARE NO WARRANTIES, EXPRESSED OR IMPLIED.  THE PERSON USING THIS SOFTWARE BEARS ALL RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE.  JASON H. MOORE AND SOFTWARE VISIONS SHALL NOT BE LIABLE FOR ANY INDIRECT, CONSEQUENTIAL, OR INCIDENTAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE.


Copyright Notice

Fractal DNA Imager, Copyright (c) 1994 by Jason H. Moore

ALL RIGHTS RESERVED

Fractal DNA Imager (TM) and Software Visions (TM)

are trademarks owned by Jason H. Moore


 Overview

DNA sequence information is usually represented and communicated via the traditional letter-based code of A, T, G and C.  Although adequate for many aspects of DNA sequence analysis, this coding is less than ideal for identifying and characterizing specific or unique patterns in the ordering of the nucleotides.  In response to this problem several graphical-based methods have been developed (see Selected Papers for several examples).

Fractal DNA Imager 1.0 is a Windows utility that translates letter-based DNA sequences (i.e. ATGC) into graphical images that facilitate the detection and characterization of  nucleotide patterns.  The algorithm used is based on a method presented previously by M. A. Gates (1986).  With this approach, each of the four nucleotide types is assigned a vector direction on a 2-dimensional grid.  As the DNA sequence is read one nucleotide at a time, the vectors are connected and the final result is a sequence-specific image.


Working With DNA Sequences

DNA sequences can be loaded from text files (*.txt), entered directly into the sequence window or generated randomly.  The sequences can be uppercase or lowercase and must be less than 30,000 bps in length.  If you choose to edit the sequence from the sequence window you can use Cntrl+C to copy, Cntrl+X to cut and Cntrl+V to paste.  Other sequence editing functions are not available at this time.  The first grouping of command buttons on the toolbar are for working with DNA sequences.  The functions of these command buttons are defined below.

 	Open Sequence Window:  This command button opens the sequence window or brings the window into focus if it is already open.

Clear Sequence Window:  The trash can button clears the current DNA sequence from the sequence window.

Generate Random Sequence:  This command button opens the random sequence window.  Simply enter the length of the desired random sequence.  A random-number generator seeded with values returned from the clock is used to generate the random sequence.  The maximum sequence length is 30,000 bps.

Open Sequence:  Pressing this command button brings up an open file dialog box.  Sequences should be in the text only (*.txt) file format.

Save Sequence As:  This command button brings up a save file as dialog box.  Sequences should be saved in the text only (*.txt) file format.

Print Sequence:  The printer button brings up a print dialog box for printing the DNA sequence shown in the sequence window.


Imaging DNA Sequences

To image a sequence, open or enter a sequence in the sequence window, set the scale (5-1000), open the image window and click inside the window with the mouse pointer.  The sequence image will then be generated.  Vector colors and nucleotide assignments can be set from the key window.  Up to four markers and their colors can be set from the marker window to identify specific vectors.  Images can then be saved to a paint file (*.bmp) or printed.  The second set of command buttons is for working with sequence images.  These buttons are defined below.

Sequence Image Window:  This command button opens the sequence image window or brings the window into focus if it is already open.

Clear Image Window:  Clicking the trash can clears the current image(s) from the image window.

Vector Key Window:  Clicking the key button opens the vector key window.  To set the vector colors simply click on the vectors.  To change the nucleotide assignments click on the nucleotides.

Marker Window:  This command button opens the marker window.  Up to four markers can be set by entering the nucleotide position.  To set the color of the marker click on the marker circle.

Save Image As:  This command button brings up the save as dialog box.  Sequence images can be saved to paint files (*.bmp).

Print Sequence Image:  Clicking the printer button brings up the print dialog box.  The image can be printed in black and white or color depending on the type of printer.

Set Scale:  This control allows you to set the scale of the image.  The scale ranges from 5 to 1000 and can be changed by clicking the left and right arrows.

Length Window:  This window reports the length of the imaged sequence in base pairs (bp).

Fractal Dimension (D) Window:  This window reports the fractal dimension (D) of the sequence image as described by Gates (1986).

Status Window:  This window reports the status of the imaging and printing processes.


Selected Journals and Papers
Selected Papers

The following is a list of selected papers with topics related to the visualization of DNA sequence patterns.  A more comprehensive bibliography of papers is available upon request to registered users.

1)  Gates, MA.  A simple way to look at DNA.  Journal of Theoretical Biology 119; 319-328 (1986).

2)  Hamori, E.  Novel DNA sequence representations.  Nature 314; 585 (1985).

3)  Jeffrey, HJ.  Chaos game representation of gene structure.  Nucleic Acids Research 18; 2163-2170 (1990).

4)  Pickover, CA.  DNA vectorgrams:  Representation of cancer genes as movements on a 2D cellular lattice.  IBM Journal of Research and Development 31; 111-118 (1987).