The MAR-Wiz tool aims at discovering the presence of Matrix
Association Regions, or MARs, within DNA sequences. MARs constitute a significant
functional block within sequences and facilitate the processes of differential
gene expression and DNA replication. Our computational approach to finding MARs is based upon the co-occrrence of 20 DNA patterns that have been known to occur in the neighborhood of MARs. These motifs are used to define higher order rules defined using the various combinations
in which the patterns have been known to co-occur. The mathematical density of the rule occurrences iin a regions is assumed to imply the presence of a MAR in that region.
This web-based tool supports the capability of uploading the DNA sequence to be analyzed from the user's machine. Your DNA sequence specified in any of the following format, If you choose to cut and paste your DNA sequence, the browser will impose a limit on the seqeunce size (around 25,000 characters).
- FASTA
- GenBank
- Plain, i.e. raw sequence
The results of MAR discovery algorithm are presented using the following:
- Version 1.0: A static GIF image of the potential showing the regions of MARs. The maximum size of the sequence processed for this option in 100,000 bp.
- Version 1.5: A scrollable Java applet that can zoom in/out and enables the user to specify the display start coordinates. The maximum sequence size processed with this option is 500,000 bp.