A web site for the analysis of yeast regulatory sequences
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A series of computer programs have been developed to address the problem
of analysing regulatory sequences, with a special focus on yeast. These
tools are publicly available on the web:
http://copan.cifn.unam.mx/Computational_Biology/yeast-toolshttp://alize.ulb.ac.be/~YRT/
Basically, three classical problems can be addressed. (i) Pattern
search: search for known regulatory elements in known upstream regions.
(ii) Pattern extraction: search for unknown regulatory elements in a set
of known upstream regions. (iii) Genome-scale pattern search: search for
genes putatively regulated by a known regulatory element.
The program feature-map allows automatically generates graphical
representations of the matching positions of multiple patterns among
multiple upstream sequences.
The site also provides a series of general utilities, such as generation
of random sequence (random-seq), automatic drawing of XY graphs from
numeric data (XYgraph), inter-conversions between various sequence
formats (convert-seq).
Several tools are linked together in order to allow their sequential
utilisation (piping), but each one can also be used independently by
filling the web form with external data. For instance, any user-entered
DNA sequence can be submitted to pattern searching or pattern
extraction. The feature-map accepts several types of data for input:
Swissprot, Transfac, regulonDB, MatInspector, Signal Scan, Patser, Gibbs
sampler, dssp. This widens the scope of the site to the analysis of
non-regulatory and/or non-yeast sequences.
Comments and suggestions are welcome.
Jacques van Helden <jvanheld at ebi.ac.uk>
European Bioinformatics Institute
