Home News About Us Contact Contributors Disclaimer Privacy Policy Help FAQ

Quick Search
My eDoc
Session History
Support Wiki
Direct access to
document ID:

          Institute: MPI für biologische Kybernetik     Collection: Biologische Kybernetik     Display Documents

ID: 312036.0, MPI für biologische Kybernetik / Biologische Kybernetik
ARTS: Accurate Recognition of Transcription Starts in Human
Authors:Sonnenburg, S.; Zien, A.; Rätsch, G.
Date of Publication (YYYY-MM-DD):2006-07
Title of Proceedings:Proceedings of the 14th International Conference on Intelligent Systems for Molecular Biology
Start Page:e472
End Page:e480
Physical Description:9
Audience:Not Specified
Intended Educational Use:No
Abstract / Description: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.
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%).
Datasets, model selection results, whole genome predictions, and additional experimental results are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/arts
External Publication Status:published
Document Type:Conference-Paper
Communicated by:Holger Fischer
Affiliations:MPI für biologische Kybernetik/Empirical Inference (Dept. Schölkopf)
The scope and number of records on eDoc is subject to the collection policies defined by each institute - see "info" button in the collection browse view.