A web site for the computational analysis of yeast regulatory sequences

✍ Scribed by van Helden, J.; Andr�, B.; Collado-Vides, J.

• Publisher: John Wiley and Sons
• Year: 2000
• Tongue: English
• Weight: 248 KB
• Volume: 16
• Category: Article
• ISSN: 0749-503X
• DOI: 10.1002/(sici)1097-0061(20000130)16:2<177::aid-yea516>3.0.co;2-9

✦ Synopsis

A series of computer programs were developed for the analysis of regulatory sequences, with a special focus on yeast. These tools are publicly available 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 patterns in the upstream regions of known genes; (b) discovery of unknown regulatory patterns within a set of upstream regions known to be co-regulated; (c) search for unknown genes potentially regulated by a known transcription factor. Each of these tasks can be performed on basis of a simple (string) or more re®ned (matrix) description of the regulatory patterns. A feature-map program automatically generates visual representations of the positions at which patterns were found. The site also provides a series of general utilities, such as generation of random sequence, automatic drawing of XY graphs, interconversions between sequence formats, etc. Several tools are linked together to allow their sequential utilization (piping), but each one can also be used independently by ®lling the web form with external data. This widens the scope of the site to the analysis of nonregulatory and/or non-yeast sequences.