To improve the detection of nucleotide sequence signals (e.g. promoter elements) by position-weight matrices (PWM) using the concept of statistically significant matches. The Mksite program was originally developed for analyzing protein sequences. We report NMksite, a new version adapted to the processing of nucleotide sequences. NMksite creates PWM from nucleotide sequence block alignments or occurrence tables using three weight computation schemes. An original feature of NMksite is the numerical computation of the statistical significance of PWM matches. The utility of this concept is demonstrated in the context of the prediction of splice sites and promoter regions. Mksite and other components of the MODEST (Motif DEsign and Search Tool) package (written in C/Unix) are available at http://igs-server.cnrs-mrs.fr E-mail: [email protected]

We describe a new technique for the automatic detection and characterization, in terms of location, size and intensity, of positive hybridization spots on hybridization filter images. We will also discuss how this information can be used to reconstruct the spot deposition pattern on the filter and thus identify the spots. The part of the algorithm dedicated to the detection of spots is derived from a technique used in astronomy for the automatic recognition of galaxies on photographic plates. This technique has been modified so that it becomes able to cope with the strongly varying background typical of hybridization filter images. The technique does not require any human intervention.