C-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression.

ABSTRACT:

Background

Computational methods for characterizing novel transcription factor binding sites search for sequence patterns or "motifs" that appear repeatedly in genomic regions of interest. Correlation-based motif finding strategies are used to identify motifs that correlate with expression data and do not rely on promoter sequences from a pre-determined set of genes.

Results

In this work, we describe a method for predicting motifs that combines the correlation-based strategy with phylogenetic footprinting, where motifs are identified by evaluating orthologous sequence regions from multiple species. Our method, c-REDUCE, can account for variability at a motif position inferred from evolutionary information. c-REDUCE has been tested on ChIP-chip data for yeast transcription fa

SUBMITTER: Kechris K 

PROVIDER: S-EPMC2626603 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature