Computational Prediction of Regulatory Elements in DNA by Comparative Sequence Analysis 

With many vertebrate genomes completed or on the near horizon, the most promising methods for predicting functional sequence elements are based on comparison of sequences from multiple species. We begin with a brief survey of computational tools appropriate for the prediction of novel regulatory elements in DNA by comparative sequence analysis, including one tool called FootPrinter designed specifically for this task. We then turn to problems that arise when using such tools on a genome-wide scale in the vertebrates. These problems include difficulties in finding reliably homologous promoter sequences, difficulties in choosing the best tool and parameters to apply to these sequences, and difficulties in assessing the significance of predictions produced. Solutions are offered to each of these problems, though they are far from complete. 

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Martin Tompa 
Department of Computer Science and Engineering 
Box 352350 
University of Washington 
Seattle, WA 98195-2350 

 

Martin Tompa - Biosketch

 Martin Tompa graduated from Harvard University in 1974 and received his Ph.D. in Computer Science from the University of Toronto in 1978. For the next 7 years he was on the Computer Science faculty at the University of Washington, where he received an NSF Presidential Young Investigator Award in 1984, the inaugural year for these awards. From 1985 to 1989 he was on the staff of the IBM Research Division at the Thomas J. Watson Research Center, and became manager of its Theory of Computation group. In 1989 he rejoined the Computer Science faculty at UW, and in 1998 and 1999 received the department's first two ACM Undergraduate Teaching Awards. Martin's research interests are in Computational Molecular Biology, with emphasis on biological sequence analysis.