Bioinformatics Seminar

Paola Bonizzoni, Associate Professor, Dipartimento di Informatica Sistemistica e Comunicazione Universit Degli Studi di Milano-Bicocca, Milan, Italy will give a seminar entitled Novel Method to Predict the Exon-Intron Structure of a Gene that is Optimally Compatible to a Set of Transcript Sequences on Monday August 22, 2005 at 3:00pm. The seminar will be held in Rm X530, UBC ICICS (INSTITUTE FOR COMPUTING, INFORMATION AND COGNITIVE SYSTEMS), 2366 Main Mall.

Abstract:
Alternative splicing (AS) is currently considered as one of the main mechanisms able to explain the huge gap between the number of predicted genes and the high complexity of proteome in humans. The rapid growth of ESTs data has encouraged the development of computational methods to predict alternative splicing from the analysis of ESTs alignment to genome sequences. I present a novel computational method to predict gene structure and (AS) from EST/transcript data based on EST against genome alignment and graph-theoretic analysis of transcripts data.

The problem of predicting constitutive and alternative splicing is formalized as an optimization problem, where the optimal multiple transcript alignment minimizes the number of exons and hence of splice site observations. A splice site predictor based on this new approach to AS prediction is implemented in the software tool ASPIC (Alternative Splicing PredICtion). Extensive bench marking showed that ASPIC outperforms other existing methods in the detection of novel splicing isoforms, in minimizing over-predictions and requiring a lower computation time for processing a single gene and an EST cluster. An experimental analysis of ASPIC prediction data is discussed in the presentation.

For more information on the Bioinformatics Event Calendar, visit VanBug Event Calendar.

Posted by Dorothy Cheung at 12:09 PM on August 18, 2005