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  PALMA: Perfect Alignments using Large Margin Algorithms

Rätsch, G., Hepp, B., Schulze, U., & Ong, C. (2006). PALMA: Perfect Alignments using Large Margin Algorithms. In D. Huson, O. Kohlbacher, A. Lupas, K. Nieselt, & A. Zell (Eds.), German Conference on Bioinformatics 2006 (GCB 2006) (pp. 104-113). Bonn, Germany: Gesellschaft für Informatik.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-D04D-D Version Permalink: http://hdl.handle.net/21.11116/0000-0004-99E8-A
Genre: Conference Paper

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GCB-2006-Raetsch.pdf (Any fulltext), 346KB
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 Creators:
Rätsch, G1, Author              
Hepp , B, Author
Schulze , U1, Author
Ong, CS2, 3, Author              
Affiliations:
1Friedrich Miescher Laboratory, Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, DE, ou_2575692              
2Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
3Max Planck Institute for Biological Cybernetics, Max Planck Society, Spemannstrasse 38, 72076 Tübingen, DE, ou_1497794              

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 Abstract: 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 http://www.fml.mpg.de/raetsch/projects/palma.

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 Dates: 2006-09
 Publication Status: Published in print
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 Rev. Method: -
 Identifiers: BibTex Citekey: 4157
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Title: German Conference on Bioinformatics (GCB 2006)
Place of Event: Tübingen, Germany
Start-/End Date: 2006-09-19 - 2006-09-22

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Title: German Conference on Bioinformatics 2006 (GCB 2006)
Source Genre: Proceedings
 Creator(s):
Huson, D, Editor
Kohlbacher, O, Editor
Lupas, A, Editor
Nieselt, K, Editor
Zell, A, Editor
Affiliations:
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Publ. Info: Bonn, Germany : Gesellschaft für Informatik
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: 104 - 113 Identifier: ISBN: 978-3-88579-177-5