Academic Journal
KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences
| العنوان: | KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences |
|---|---|
| المؤلفون: | Sebastian J. Schultheiss, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, Gunnar Rätsch |
| المساهمون: | The Pennsylvania State University CiteSeerX Archives |
| المصدر: | http://www.bx.psu.edu/old/courses/bx-fall09/KIRMES.pdf. |
| سنة النشر: | 2009 |
| المجموعة: | CiteSeerX |
| الوصف: | Motivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor binding sites in promoter regions of potential transcription factor target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cisregulatory modules. Results: We propose a new algorithm that combines the benefits of existing motif finding with the ones of Support Vector Machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of transcription factor targets. Availability: The PYTHON source code (open source–licensed under GPL), the data for the experiments and a Galaxy-based web service are available at |
| نوع الوثيقة: | text |
| وصف الملف: | application/pdf |
| اللغة: | English |
| Relation: | http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.413.9349; http://www.bx.psu.edu/old/courses/bx-fall09/KIRMES.pdf |
| الاتاحة: | http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.413.9349 http://www.bx.psu.edu/old/courses/bx-fall09/KIRMES.pdf |
| Rights: | Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
| رقم الانضمام: | edsbas.69131375 |
| قاعدة البيانات: | BASE |
| الوصف غير متاح. |