Bio-informatics Project

Pattern matching algorithms have direct applications in many bioinformatics problems. Some examples include searching for different kinds of motifs, designing unique oligonucleotides for micro arrays and multiple sequence alignment. As our lab¡¯s expertise is in data compression and pattern matching, we feel that we can contribute to this area of bioinformatics.

Currently, one full-time Ph.D. student is working in this area, looking for potential problems to solve and acquiring the biological knowledge necessary to understand the problems in this area.

Current Projects

1. Codon Optimization

This project deals with designing synthetic DNA vaccines by controlled modification of a natural vaccine, by enhancing certain properties of the vaccine. Specifically, it deals with codon optimizing the DNA vectors for a target species, and maximizing/minimizing certain motifs. This problem has been mapped to the problem of finding the longest weighted path in a directed acyclic graph. A paper on this project, ¡°A pattern matching algorithm for codon optimization and CpG-motif engineering in DNA expression vectors¡± was presented at the IEEE computer society bioinformatics conference (CSB 2003, Aug 11-14, Stanford). Full Paper

2. Automatic Annotation of Mu-TAIL PCR Flank Sequences

In this project, we are working with researchers in Biology at the University of Florida. The goal of the project is to develop tools that assist in analyzing experimental data in order to identify genes that effect the development of the maize endosperm.

3. Finding Monad patterns in DNA sequences

We developed new algorithms for finding trascription factor binding sites. The algorithms, named PRUNER, result in an imroved complexity over the previous approaches.

Other areas of interest

¡¤ Designing probes for micro arrays


For more information, please contact Dr. Amar Mukherjee


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