- Article -
| In Silico Biology 4, 0040 (2004); ©2004, Bioinformation Systems e.V. |
Annotating significant pairs of transcription factor binding sites in regulatory DNA
Katja Rateitschak1*, Tobias Müller2 and Martin Vingron
Max Planck Institute for Molecular Genetics
Ihnestr. 73, D-14195 Berlin, Germany
Email: Katja.Rateitschak@molgen.mpg.de, Tobias.Mueller@molgen.mpg.de, Martin.Vingron@molgen.mpg.de
1 Present address: Max Planck Institute of Colloids and Interfaces, D-14424 Potsdam, Germany
2 Present address: Department of Bioinformatics, Biozentrum, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
* corresponding author
Edited by E. Wingender; received May 21, 2004; revised and accepted August 10, 2004; published August 20, 2004
Abstract
In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score based on TRANSFAC-matrices together with a score based on pairs of BS. The latter score positively weights pairs of BS that tend to occur together in many regulatory DNA-sequences, in contrast to a random background model. The empirical BS pair frequencies result from our evaluation of a large dataset of orthologous genes.
Key words: recognition of genes and regulatory elements, transcription factor binding site, score matrix