MATIND AND MATINSPECTOR - NEW FAST AND VERSATILE TOOLS FOR DETECTION OF CONSENSUS MATCHES IN NUCLEOTIDE-SEQUENCE DATA

The identification of potential regulatory motifs in new sequence data is increasingly important for experimental design. Those motifs are c ommonly located by matches to IUPAC strings derived from consensus seq uences. Although this method is simple and widely used, a major drawba ck of IUPAC strings is that they necessarily remove much of the inform ation originally present in the set of sequences. Nucleotide distribut ion matrices retain most of the information and are thus better suited to evaluate new potential sites. However, sufficiently large librarie s of pre-compiled matrices are a prerequisite for practical applicatio n of any matrix-based approach and are just beginning to emerge. Here we present a set of tools for molecular biologists that allows generat ion of new matrices and detection of potential sequence matches by aut omatic searches with a library of pre-compiled matrices. We also suppl y a large library (>200) of transcription factor binding site matrices that has been compiled on the basis of published matrices as well as entries from the TRANSFAC database, with emphasis on sequences with ex perimentally verified binding capacity. Our search method includes pos ition weighting of the matrices based on the information content of in dividual positions and calculates a relative matrix similarity. We sho w several examples suggesting that this matrix similarity is useful in estimating the functional potential of matrix matches and thus provid es a valuable basis for designing appropriate experiments.