PALMA: Perfect alignments using large margin algorithms
| dc.contributor.author | Rätsch, G. | |
| dc.contributor.author | Hepp, B. | |
| dc.contributor.author | Schulze, U. | |
| dc.contributor.author | Ong, C. S. | |
| dc.contributor.editor | Huson, Daniel | |
| dc.contributor.editor | Kohlbacher, Oliver | |
| dc.contributor.editor | Lupas, Andrei | |
| dc.contributor.editor | Nieselt, Kay | |
| dc.contributor.editor | Zell, Andreas | |
| dc.date.accessioned | 2019-08-12T13:06:16Z | |
| dc.date.available | 2019-08-12T13:06:16Z | |
| dc.date.issued | 2006 | |
| dc.description.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. | en |
| dc.identifier.isbn | 978-3-88579-177-5 | |
| dc.identifier.pissn | 1617-5468 | |
| dc.identifier.uri | https://dl.gi.de/handle/20.500.12116/24204 | |
| dc.language.iso | en | |
| dc.publisher | Gesellschaft für Informatik e.V. | |
| dc.relation.ispartof | German Conference on Bioinformatics | |
| dc.relation.ispartofseries | Lecture Notes in Informatics (LNI) - Proceedings, Volume P-83 | |
| dc.title | PALMA: Perfect alignments using large margin algorithms | en |
| dc.type | Text/Conference Paper | |
| gi.citation.endPage | 113 | |
| gi.citation.publisherPlace | Bonn | |
| gi.citation.startPage | 104 | |
| gi.conference.date | September 19-22, 2006 | |
| gi.conference.location | Tübingen | |
| gi.conference.sessiontitle | Regular Research Papers |
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