PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

PALMA: Perfect Alignments using Large Margin Algorithms
Gunnar Raetsch, Bettina Hepp, Uta Schulze and Cheng Soon Ong
In: German Conference on Bioinformatics, 20-22 Sept 2006, Tuebingen, Germany.


Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. We present a novel approach based on large margin learning that combines kernel based splice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm -- called PALMA -- tunes the parameters of the model such that the true alignment scores higher than all other alignments. In an experimental study on the alignments of mRNAs containing artificially generated micro-exons, we show that our algorithm drastically outperforms all other methods: It perfectly aligns all 4358 sequences on an hold-out set, while the best other method misaligns at least 90 of them. Moreover, our algorithm is very robust against noise in the query sequence: when deleting, inserting, or mutating up to 50% of the query sequence, it still aligns 95% of all sequences correctly, while other methods achieve less than 36% accuracy. For datasets, additional results and a stand-alone alignment tool see

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EPrint Type:Conference or Workshop Item (Paper)
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Learning/Statistics & Optimisation
ID Code:2316
Deposited By:Cheng Soon Ong
Deposited On:18 November 2006