The Role of Algorithmic Research in Computational Genomics算法研究在计算基因组学中的作用.pptVIP

The Role of Algorithmic Research in Computational Genomics Richard M. Karp IEEE Computer Society Bioinformatics Conference August 14, 2003 Algorithmic Research in Computer Science Computer science is a ``science of the artificial.’’ Problems are precisely stated and are often generic rather than application-specific. The quality of an algorithm is measured by its worst-case time bound. Mathematical elegance is just as important as relevance to applications. Algorithmic Research in Computational Genomics The goal is to understand ground truth. Problem statements are often fuzzy. Problems are often application-specific, and problem formulations must be faithful to those applications. The quality of an algorithm is measured by its performance on real data. Biological findings are more important than computational methods. Genomics can Benefit from Algorithmic Research in C.S. Data structures such as suffix trees. Randomized algorithms and sampling techniques. Dynamic programming (sequence alignment, RNA folding, protein threading, haplotype block structure…) Network flows, graph theory, NP-completeness, integer programming, semidefinite programming. Adapting to Genomics Choose problems that are fundamental, timely and relevant. Mathematical depth and elegance are highly desirable, but often simple mathematics, artfully applied, is the key to success. Avoid problems that will change when technology changes. Learn the biological background of your problem, the available sources of data and their noise characteristics. Adapting to Genomics Work with an application-oriented team and don’t get typecast as an algorithms specialist. Benchmark your algorithms on real data, establish a user community and make your software available and easy to use. Sequence Assembly Given many noisy `reads’ of short substrings of a target string, identify the target string. The shortest superstring problem, an elegant but flawed abstraction: find a shortest string containing a set of given