This talk is a dry run talk. The speaker, Abel Licon, will present the paper at HiCOMB 2008, the Seventh IEEE International Workshop on High Performance Computational Biology on Monday, April 14, 2008 at the Hyatt Regency Resort, in Miami Florida, USA. More information about the paper:
Title: On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks
Auhtors: Michela Taufer (1), Thamar Solorio (2), Abel Licon (1, 3), David Mireles (3), and Ming-Ying Leung (4)
Affiliations:
(1)Department of Computer & Information Sciences, University of Delaware
(2)Department of Computer of Science, The University of Texas at Dallas
(3)Department of Computer Science, The University of Texas at El Paso
(4)Department of Mathematical Sciences and Bioinformatics Program, The University of Texas at El Paso
Abstract:
Despite the computing power of emerging technologies, predicting long
RNA secondary structures with thermodynamics-based methods is still
infeasible, especially if the structures include complex motifs such
as pseudoknots.
This paper presents preliminary results on rebuilding RNA secondary
structures by an extensive and systematic sampling of nucleotide
chunks. The rebuilding approach merges the significant motifs found in
the secondary structures of the single chunks. The extensive sampling
and prediction of nucleotide chunks are supported by grid technology
as part of the RNAVLab functionality. Significant motifs are
identified in the chunk secondary structures and merged in a single
structure based on their recurrences and other statistical insights. A
critical analysis of the strengths, weaknesses, and future
developments of our method is presented.