A web site for the computational analysis of yeast regulatory sequences

A series of computer programs were developed for the analysis of regulatory sequences, with a special focus on yeast. These to ols are publicly availa ble on the web (http://copan.cifn.unam.mx/Computational_Biology/yeast-tools or http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/). Basically, three classical problems can be addressed: (a) search for known regulatory patter ns in the upstream regions of known genes; (b) discovery of unknown regulat ory patterns within a set of upstream regions known to be co-regulated; (c) search for unknown genes potentially regulated by a known transcription fa ctor. Each of these tasks can be performed on basis of a simple (string) or more refined (matrix) description of the regulatory patterns. A feature-ma p program automatically generates visual representations of the positions a t which patterns were found. The site also provides a series of general uti lities, such as generation of random sequence, automatic drawing of XY grap hs, interconversions between sequence formats, etc. Several tools are linke d together to allow their sequential utilization (piping), but each one can also be used independently by filling the web form with external data. Thi s widens the scope of the site to the analysis of nonregulatory and/or non- yeast sequences. Copyright (C) 2000 John Wiley & Sons, Ltd.