Bioinformatics Research Group

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Our research group designs, develops and assesses computational tools for the exploration of genomic and proteomic data. As computer scientists, we also study algorithmic questions inspired by and related to biological problems. Finally, we collaborate with biologists to study the usefulness in practice of the methods we develop. Featured Research Project Spaced Seeds for Homology Search Homology search is the task of finding pairs of similar substrings in large DNA or protein sequence databases. Such sequence alignments highlight areas that may be preserved by evolution and help to determine their biological function. BLAST, a popular heuristic program for this task, is a household name among biologists. In 2002, we introduced the technique of spaced seeds for increasing the accuracy and speed of BLAST-like algorithms. We have studied mathematical properties of spaced seeds, related algorithmic problems, and selection of appropriate spaced seeds for particular tasks. The resultant commercial tool, PatternHunter, was used to compare the human and mouse genomes by the Mouse Genome Sequencing Consortium. Most recently, we are combining homology search with gene finding to find homologs of a known gene in other organisms. Bin Ma, John Tromp, Ming Li. PatternHunter: faster and more sensitive homology search. Bioinformatics, 2002. Details Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature, 2002. (Daniel Brown and Ming Li are members of MGSC). Details Daniel G. Brown, Ming Li, Bin Ma. A tutorial of recent developments in the seeding of local alignment. Journal of Bioinformatics and Computational Biology, 2004. Details Brona Brejova, Daniel G. Brown, Tomas Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 2005. Early version appeared in WABI 2003. Details Ming Li, Bin Ma, Zhang Louxin. Superiority and complexity of the spaced seeds. In Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithms (SODA 2006), 2006. Details View more papers on: spaced seeds, homology search

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