 Logo of narLink to Publisher's site Nucleic Acids Res. 2006
December; 34(22): 6379–6391. Published online 2006 November 27.
doi:  10.1093/nar/gkl658 PMCID: PMC1702486  Identification of
degenerate motifs using position restricted selection and hybrid
ranking combination   The identification of regulatory elements
recognized by transcription factors and chromatin remodeling
factors is essential to studying the regulation of gene
expression. When no auxiliary data, such as orthologous
sequences or expression profiles, are used, the accuracy of most
tools for motif discovery is strongly influenced by the motif
degeneracy and the lengths of sequence. Since suitable auxiliary
data may not always be available, more work must be conducted to
enhance tool performance to identify transcription elements in
the metazoan. A non-alignment-based algorithm, MotifSeeker, is
proposed to enhance the accuracy of discovering degenerate
motifs. MotifSeeker utilizes the property that variable sites of
transcription elements are u