Using and developing bioinformatics tools
to elucidate the evolution of proteins

Rahul Karnik
Advisor: Dr. A. Malcolm Campbell
Second reader: Dr. David Wessner


The rapid growth of protein sequence databases has presented an opportunity to find evolutionary relationships and common functional domains between proteins. We present a systematic method of investigation using publicly available software tools to search for such relationships. Also presented is a new program, Divide-and-BLAST, which uses a divide-and-conquer algorithm in conjunction with the Basic Alignment and Search Tool (BLAST) program to detect remote similarities that are usually not seen in normal BLAST output. The system was tested using two proteins, isocitrate dehydrogenase 1 (IDH1) and caspase 3 (apopain), and yielded results that could be used to direct further study.

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