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

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public data base. The large volume, high degree of fragmentation and lack of gene struc ture annotations prevent efficient and effective searches of HTG and EST da ta for protein sequence homologies by standard search methods. Here, we bri efly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especial ly to biologists not having access to a powerful local bioinformatics envir onment. 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 prec omputed matches between protein sequences (including sequences from trEST a nd trGEN) and patterns and profiles from Prosite and Pfam. The three resour ces can be accessed via the Hits home page (http://hits.isb-sib.ch).