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Nucleic Acids Research, 2002, Vol. 30, No. 1 299-300
© 2002 Oxford University Press

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein

Antje Krause*, Stefan A. Haas, Eivind Coward and Martin Vingron

Max-Planck-Institute for Molecular Genetics, Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The SYSTERS protein sequence cluster set provides an automatically generated classification of all sequences of the SWISS-PROT, TrEMBL and PIR databases into disjoint protein family and superfamily clusters. GeneNest is a database and software package for producing and visualizing gene indices from ESTs and mRNAs. Currently, the database comprises gene indices of human, mouse, Arabidopsis thaliana and zebrafish. SpliceNest is a web-based graphical tool to explore gene structure, including alternative splicing, based on a mapping of the EST consensus sequences from GeneNest to the complete human genome. The integration of SYSTERS, GeneNest and SpliceNest into one framework now permits an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. The databases are available for querying and browsing at http://cmb.molgen.mpg.de.

* To whom correspondence should be addressed. Tel: +49 30 8413 1404; Fax: +49 30 8413 1152; Email: krause_a{at}molgen.mpg.de


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