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Activity Number: 510
Type: Contributed
Date/Time: Thursday, August 10, 2006 : 8:30 AM to 10:20 AM
Sponsor: Biopharmaceutical Section
Abstract - #306192
Title: A Sequential Monte Carlo EM Solution to the Transcription Factor Binding Site Identification Problem
Author(s): Edmund Jackson*+ and William Fitzgerald
Companies: Cambridge University and Cambridge University
Address: Trinity College, Cambridge, CB21TQ, UK
Keywords: sequential Monte Carlo ; transcription factor binding sites ; expectation maximization ; sequence analysis
Abstract:

A significant and stubbornly intractable problem in genome sequence analysis has been the identification of novel transcription factor binding sites in promoter regions. Probabilistic methods have faced difficulties from prior ignorance and poor models of the biological sequence. In addition, this inference problem occurs in an extremely irregular, high dimensional space. In order to overcome this problem we propose utilizing an iterated particle optimization in place of the standard Gibbs sampling approach. We derive and demonstrate this novel method and show improved convergence to the global mode.

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