Robust Tools for Biological Sequence Analysis

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A grant has been awarded to the University of Arizona to develop a computer program to use a new and novel way of aligning protein sequences, especially those of whole genomes. The program will focus on two of the most daunting issues in aligning gene sequences: very specifically aligning small areas of protein sequences and less specifically but very defensibly aligning many sequences together. The proposal is to develop a robust and integrated suite of open-source tools to do both local and multiple alignments using a computer science technique that is novel in this arena and that yields exact algorithms guaranteed to find optimal solutions. The resulting algorithms will be carefully tested using both real data with published benchmarks and simulated data with known optimal alignments.