CAREER: New Technologies for Biosequence Comparison

Washington University, Saint Louis MO

Investigators

Abstract

Computational comparison of biosequences is fundamental to modern biology. It is the fastest, most widely used technology to annotate the functional elements of a newly sequenced genome. Algorithms for comparison must address the rapid increase in the size of sequence databases and the need for more sensitive tools of multiple alignments, as well as the need to compare inferred feature models. Enhancing the pattern-matching algorithms that form the heart of fast comparison tools is the focus of this research. A research framework for rational pattern design and a technique for combining pattern matching with substitution score matrices will be incorporated. Pattern matching generalizes the word-matching heuristics of alignment algorithms. The choice of pattern can impact the search speed and sensitivity. The improved search patterns will be specialized to particular feature types, such as coding sequence, or to groups of organisms. Collaborations with popular search tool developers are established and will help integrate the new methods. Research training involves students at many levels and will also form the basis of cross-disciplinary student exchanges.