Premium
A web site for the computational analysis of yeast regulatory sequences
Author(s) -
van Helden J.,
André B.,
ColladoVides J.
Publication year - 2000
Publication title -
yeast
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.923
H-Index - 102
eISSN - 1097-0061
pISSN - 0749-503X
DOI - 10.1002/(sici)1097-0061(20000130)16:2<177::aid-yea516>3.0.co;2-9
Subject(s) - biology , regulatory sequence , computational biology , set (abstract data type) , string (physics) , web server , computer science , genetics , gene , transcription factor , the internet , world wide web , programming language , physics , quantum mechanics
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 refined (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 filling the web form with external data. This widens the scope of the site to the analysis of non-regulatory and/or non-yeast sequences.