Abstract
We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. As in previous editions the genetic names are consistently associated to each sequence with a known and confirmed ORF. If necessary, synonyms are given in the case of allelic duplicated sequences. Although the first publication of a sequence gives-according to our rules-the genetic name of a gene, in some instances more commonly used names are given 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 synonyms 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 the systematic sequencing efforts. Since the release of LISTA4.1 we update the database continuously. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. This release includes reports from full Smith and Watermann peptide-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). The database is available by FTP and on World Wide Web.
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Selected References
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- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Bennetzen J. L., Hall B. D. Codon selection in yeast. J Biol Chem. 1982 Mar 25;257(6):3026–3031. [PubMed] [Google Scholar]
- Collins J. F., Coulson A. F. Significance of protein sequence similarities. Methods Enzymol. 1990;183:474–487. doi: 10.1016/0076-6879(90)83032-5. [DOI] [PubMed] [Google Scholar]
- Dölz R., Mossé M. O., Slonimski P. P., Bairoch A., Linder P. LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces. Nucleic Acids Res. 1994 Sep;22(17):3459–3461. doi: 10.1093/nar/22.17.3459. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Etzold T., Argos P. SRS--an indexing and retrieval tool for flat file data libraries. Comput Appl Biosci. 1993 Feb;9(1):49–57. doi: 10.1093/bioinformatics/9.1.49. [DOI] [PubMed] [Google Scholar]
- Linder P., Dölz R., Mossé M. O., Lazowska J., Slonimski P. P. LISTA, a comprehensive compilation of nucleotide sequences encoding proteins from the yeast Saccharomyces. Nucleic Acids Res. 1993 Jul 1;21(13):3001–3002. doi: 10.1093/nar/21.13.3001. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mortimer R. K., Contopoulou C. R., King J. S. Genetic and physical maps of Saccharomyces cerevisiae, Edition 11. Yeast. 1992 Oct;8(10):817–902. doi: 10.1002/yea.320081002. [DOI] [PubMed] [Google Scholar]
- Mosse M. O., Brouillet S., Risler J. L., Lazowska J., Slonimski P. P. A comprehensive compilation of 400 nucleotide sequences coding for proteins from the yeast Saccharomyces cerevisiae = LISTA1. Curr Genet. 1988 Dec;14(6):529–535. doi: 10.1007/BF00434077. [DOI] [PubMed] [Google Scholar]
- Mossé M. O., Linder P., Lazowska J., Slonimski P. P. A comprehensive compilation of 1001 nucleotide sequences coding for proteins from the yeast Saccharomyces cerevisiae (= ListA2) Curr Genet. 1993 Jan;23(1):66–91. doi: 10.1007/BF00336752. [DOI] [PubMed] [Google Scholar]