Software Tools available at NMSU

CisPlot: A Grapical display tool to represent promoter regulatory elements. We designed this tool to receive an input from a file that contains the DNA sequence in a FASTA format. The file is then submitted to an on-line form of a web cis-element prediction program. In CisPlot , the user then selects the database of cis-elements to search against. Then CisPlot receives the HTML output of the prediction program. The HTML output is then parsed to get the information of the cis-elements present and their positions and whether they are present in the positive (+) or the negative (-) strand. A canvas is used in this program to display cis-elements. A unique color circle is used to represent each predicted cis-element. To get the cis-element color, its DNA sequence is hashed to get hash value which represent a color. The cis-elements on the positive strand are drawn on top of the sequence and the cis-elements on the negative strand are drawn below the sequence. User have a choice to select more DNA sequence files and can save all the graphical outputs.

The graphical display can be exported for printing in a document file. The tool is expected to be useful in comparison of promoters for allelic variants with different transcription patterns as well as generally useful as a way to display the data in a more concise and accessible manner. The tool is freeware available for download. This tool is written in java the tool will work on Windows, Mac and UNIX operating systems.

To use this tool download here.

Sytem Requirements to use CisPlot tool :

Program works with online prediction tools to display the output

This program needs access to the internet to function

CisPlot tool needs Java 1.4.2 version or higher or atleast java runtime environment.

Note: DNA sequence files must be in FASTA format.

Sample snap shots from CisPlot :

Figure A. CisPlot layout.

Figure B. Sample output from the CisPlot using PLACE signal database as source.