PALMA: Perfect alignments using large margin algorithms
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.
- Citation
- BibTeX
Rätsch, G., Hepp, B., Schulze, U. & Ong, C. S.,
(2006).
PALMA: Perfect alignments using large margin algorithms.
In:
Huson, D., Kohlbacher, O., Lupas, A., Nieselt, K. & Zell, A.
(Hrsg.),
German Conference on Bioinformatics.
Bonn:
Gesellschaft für Informatik e.V..
(S. 104-113).
@inproceedings{mci/Rätsch2006,
author = {Rätsch, G. AND Hepp, B. AND Schulze, U. AND Ong, C. S.},
title = {PALMA: Perfect alignments using large margin algorithms},
booktitle = {German Conference on Bioinformatics},
year = {2006},
editor = {Huson, Daniel AND Kohlbacher, Oliver AND Lupas, Andrei AND Nieselt, Kay AND Zell, Andreas} ,
pages = { 104-113 },
publisher = {Gesellschaft für Informatik e.V.},
address = {Bonn}
}
author = {Rätsch, G. AND Hepp, B. AND Schulze, U. AND Ong, C. S.},
title = {PALMA: Perfect alignments using large margin algorithms},
booktitle = {German Conference on Bioinformatics},
year = {2006},
editor = {Huson, Daniel AND Kohlbacher, Oliver AND Lupas, Andrei AND Nieselt, Kay AND Zell, Andreas} ,
pages = { 104-113 },
publisher = {Gesellschaft für Informatik e.V.},
address = {Bonn}
}
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More Info
ISBN: 978-3-88579-177-5
ISSN: 1617-5468
xmlui.MetaDataDisplay.field.date: 2006
Language:
(en)

Content Type: Text/Conference Paper