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  ARTS: Accurate Recognition of Transcription Starts in Human

Sonnenburg, S., Zien, A., & Rätsch, G. (2006). ARTS: Accurate Recognition of Transcription Starts in Human. Bioinformatics, 22(14): H-56, e472-e480.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0013-D0CB-F Version Permalink: http://hdl.handle.net/21.11116/0000-0004-B645-1
Genre: Conference Paper

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 Creators:
Sonnenburg, S, Author              
Zien, A1, 2, Author              
Rätsch, G3, Author              
Affiliations:
1Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497794              
2Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society, ou_1497795              
3Friedrich Miescher Laboratory, Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, DE, ou_2575692              

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 Abstract: Motivation: One of the most important features of genomic DNA are the protein-coding genes. While it is of great value to identify those genes and the encoded proteins, it is also crucial to understand how their transcription is regulated. To this end one has to identify the corresponding promoters and the contained transcription factor binding sites. TSS finders can be used to locate potential promoters. They may also be used in combination with other signal and content detectors to resolve entire gene structures. Results: We have developed a novel kernel based method - called ARTS - that accurately recognizes transcription start sites in human. The application of otherwise too computationally expensive Support Vector Machines was made possible due to the use of efficient training and evaluation techniques using suffix tries. In a carefully designed experimental study, we compare our TSS finder to state-of-the-art methods from the literature: McPromoter, Eponine and FirstEF. For given false positive rates within a reasonable range, we consistently achieve considerably higher true positive rates. For instance, ARTS finds about 24 true positives at a false positive rate of 1/1000, where the other methods find less than half (10.5). Availability: Datasets, model selection results, whole genome predictions, and additional experimental results are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/arts

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 Dates: 2006-07
 Publication Status: Published in print
 Pages: -
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 Rev. Method: -
 Identifiers: DOI: 10.1093/bioinformatics/btl250
BibTex Citekey: 3960
 Degree: -

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Title: 14th International Conference on Intelligent Systems for Molecular Biology (ISMB 2006)
Place of Event: Fortaleza, Brazil
Start-/End Date: 2006-08-06 - 2006-08-10

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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 22 (14) Sequence Number: H-56 Start / End Page: e472 - e480 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991