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Nucleic Acids Research, 2004, Vol. 32, Database issue D351-D353
© 2004 Oxford University Press

PHYTOPROT: a database of clusters of plant proteins

S. Mohseni-Zadeh, A. Louis1, P. Brézellec and J.-L. Risler*

Laboratoire Génome et Informatique, UMR 8116 and 1 Infobiogen, Tour Evry 2, 523 Place des Terrasses, 91034 Evry Cedex, France

*To whom correspondence should be addressed. Tel: +33 1 01 60 87 38 67; Fax: +33 1 01 60 87 38 97; Email: risler{at}genopole.cnrs.fr
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related proteins. Within each cluster, the sequences have been submitted to pyramidal classification; in the case where two or several subfamilies have been grouped together, the pyramidal tree helps in finding which sequences make the links between subfamilies. In addition, the ‘domains’ that are common to two or more sequences within a cluster were determined and displayed à la ProDom. The resulting graphical representations proved to be quite efficient in pinpointing those protein sequences suffering from a probable error in the annotation of their genes. The clusters can be searched through various criteria and their pyramidal classifications and their domain representations can be displayed by querying http://genoplante-info. infobiogen.fr/phytoprot. The user can also launch a BLAST search of a query sequence against all the clusters.


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