MAR-Wiz is a data mining tool that utilizes the pattern-density on DNA sequence as the basis for predicting the occurrence of Matrix Association Regions or MARs. The pattern density is based on the occurrences of patterns that have been biologically knwon to be associated with MARs. The user is allowed to select a subset of these known patterns as a basis for their prediction. Note: Currently the web tool is designed to perform analysis of sequences up to 100 kb in length. Please contact us if you would like us to run sequences larger than 100 kb.


 

DNA Sequence Entry

Enter your DNA Sequence in the text area provided. Please include only the DNA sequence data (no comments, descriptions, etc.) All blank spaces and newline characters in this window are acceptable.

Due to the data field size limitations imposed by browsers on various platforms, there exists a maximum limit of 29 kb for PC browsers. To overcome this limit please use the Sequence File Upload form.

 

Sequence File Upload Form

The Sequence File Upload Form allows the uploading of all popular DNA sequence file formats, including FASTA, GENBANK, EMBL, GCG, etc.

The Sequence Upload Form lets you select a sequence file via your web browser and allows you to upload it to the MAR-Finder server where it is analyzed by our CGI program. This form eliminates the need for copying and pasting your sequence data, and also overcomes the field file size limits of some browsers.

 

Sequence Description

If a short description is entered (optional), it will appear in the analysis results.

 

Mar Analysis Rules

     

Sliding Window Parameters

The task of detecting regions of matrix association is modeled as a problem of hypothesis testing. Since matrix association is a property of a span of the sequence, a sliding window algorithm was considered appropriate for detecting MARs . The sliding window algorithm uses two parameters, the window width and a window slide distance. These parameters can be changed from their default values of 1000 and 100, respectively.

 

Peak Detection Parameters

 

Additional Rules (Optional)

 

Summary Report

 

Find MAR (Submit) Button

Will search your sequence for MARs and display results using a GIF plot or a Java applet.