Affiliations: Max Planck Institute for Molecular Genetics, Ihnestr.
73, D-14195 Berlin, Germany. E-mail: {Katja.Rateitschak, Tobias.Mueller,
Martin.Vingron}@molgen.mpg.de
Note: [] Corresponding author. Present address: Max Planck Institute of
Colloids and Interfaces, D-14424 Potsdam, Germany
Note: [] Present address: Department of Bioinformatics, Biozentrum,
Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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.
Keywords: recognition of genes and regulatory elements, transcription factor binding site, score matrix