My research interests are Computer Science and Information Technology Education, Bioinformatics, Genomic Databases, Data Mining, Information Retrieval.

Searching genomes, even of small sizes (e.g., mitochondria or viral genomes), for query sequences (we will refer to them as probes), is computationally intensive.

My tool, probeSearch, addresses this problem. It finds exact occurrences of a given short probe in a given genome in a very short amount of time; for instance, using an old laptop with 384MB of RAM, it finds all 73,515 occurences of the probe TATAGA in the Chromosome 2 of the human genome in about half a second. probeSearch is written in native C, allowing it to ported to any computing environment. It consists of modules for the Index Generator and the Search programs.

I have developed several applications using this tool. For example, there is a version that uses probeSearch to find differentiating probes between genomes, i.e., we find all probes that are present in one genome and not in the other. Using the first version of probeSearch as a subroutine, we have also developed parallelized versions designed to run on a cluster environment. I am currently working on improved versions of probeSearch.

If you are working on a project where you think this tool may be of use, please feel free to contact me