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Nucleic Acids Research, 2001, Vol. 29, No. 1 148-151
© 2001 Oxford University Press

trEST, trGEN and Hits: access to databases of predicted protein sequences

Marco Pagni1, Christian Iseli1,3, Thomas Junier1,2, Laurent Falquet1,2, Victor Jongeneel1,3 and Philipp Bucher1,2,*

1Swiss Institute of Bioinformatics, 2Swiss Institute for Experimental Cancer Research and 3Office of Information Technology, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, CH-1066, Epalinges s/Lausanne, Switzerland

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

* To whom correspondence should be addressed at: Swiss Institute of Bioinformatics, Instititue of Experimental Cancer Research, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland. Tel: +41 21 692 59 91; Fax: +41 21 692 59 45; Email: philipp.bucher@isb-sib.ch


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