A Consensus Match Scoring System thatis Correlated with Biological Functionality

Abstract

The C;-scoring system is suitable for the identification of putative functional transcription factor binding sites solely by sequence analysis. This is a very important feature since it allows preselection of candidate bindingsites for experimental analysis from uncharacterized genomic sequences. Data derived from the analysis of almost 2.4 million nucleotides of genomic sequences show a good correlation of C;-scoring with known biological function. High-scoring bindingsites are clearly over-represented in putative control regions of the genomic sequences. Known functional bindingsites cluster in the same regions. Furthermore, we demonstrate high C;-scores to correlate with biological functionality of 26 individual binding sites for three completely unrelated transcription factors. Consensus matches knownto be either nonfunctional or to bind their correspondingprotein factors with highly reduced affinity are low-scorers in ourrating.