LISTA, LISTA-HOP AND LISTA-HON - A COMPREHENSIVE COMPILATION OF PROTEIN-ENCODING SEQUENCES AND ITS ASSOCIATED HOMOLOGY DATABASES FROM THE YEAST SACCHAROMYCES

We continued our effort to make a comprehensive database (LISTA) for t he yeast Saccharomyces cerevisiae. As in previous editions [Dolz,R., M osse,M.-O., Slonimski, P.P., Bairoch,A. and Linder,P. (1994) Nucleic A cids Res. 22, 3459-3461] the genetic names are consistently associated to each sequence with a known and confirmed ORF. If necessary, synony ms are given in the case of allelic duplicated sequences. Although the first publication of a sequence gives-according to our rules-the gene tic name of a gene, in some instances more commonly used names are giv en to avoid nomenclature problems and the use of ancient designations which are no longer used. In these cases the old designation is given as synonym. Thus sequences can be found either by the name or by synon yms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, SWISSPROT and EMBL accession numbers. New entries will also contain the name from th e systematic sequencing efforts. Since the release of LISTA4.1 we upda te the database continuously. To obtain more information on the includ ed sequences, each entry has been screened against non-redundant nucle otide and protein data bank collections resulting in LISTA-HON and LIS TA-HOP. This release includes reports from full Smith and Watermann pe ptide-level searches against a non-redundant protein sequence database . The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). T he database is available by FTP and on World Wide Web.