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Designing Secondary Structure Profiles for Fast ncRNA Identification
The Hong Kong University of Science and Technology Department of Computer Science and Engineering Department of Chemical Engineering (CENG) Human Language Technology Center JOINT SEMINAR ----------------------------------------------------------------- Speaker: Yanni SUN Washington University Title: "Designing Secondary Structure Profiles for Fast ncRNA Identification" Date: Friday, 21 December 2007 Time: 4:00pm - 5:00pm Venue: Lecture Theater F (Leung Yat Sing Lecture Theater, near lift 25/26) HKUST Abstract: Recent biological studies revealed more and more functions of non-coding RNAs (ncRNAs) in many biological processes such as tRNAs, riboswitches, and RNA interference. Annotating ncRNAs in gnome databases for biological function analysis is thus becoming increasingly important. The most widely used tool for describing ncRNA families is based on the stochastic context-free grammar (SCFG). However, the use of SCFG incurs a high computational cost, which creates a major challenge for searching ncRNAs in large-scale gnome databases. A promising approach to speed up SCFG based ncRNA search is to use filters to exclude a large portion of the database that is unlikely to contain the ncRNA of interest. In this talk, I will present a systematic framework to utilize a new filter called the secondary structure profile (SSP) that can be efficiently scanned against large databases. We use dynamic programming to estimate an SSP's sensitivity and false positive rate, which leads to an efficient and fully automated filter design algorithm. Experiments demonstrate that our SSP-based filters can achieve high sensitivity, specificity, and an average of 200x speedup for a majority of known ncRNA families. ****************** Biography: Yanni SUN is a Ph.D. candidate in the Department of Computer Science and Engineering at Washington University in St. Louis, USA. She received her BS and MS degrees in Computer Science from Xi'an Jiao Tong University, China, in 1998 and 2001 respectively. Her research interests include Bioinformatics/computational biology, pattern design, pattern search, similarity search in large-scale database. Her work has been published in prestigious academic journals including Journal of Computational Biology and BMC Bioinformatics, as well as in top Bioinformatics conferences including RECOMB and ECCB.