Abstract
We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. In this database each sequence has been attributed a single genetic name. In the case of duplicated sequences a simple method has been applied to distinguish between sequences of one and the same gene from non-allelic sequences of duplicated genes. If necessary, synonyms are given in the case of allelic duplicated sequences. 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. 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. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS).
Full text
PDFSelected References
These references are in PubMed. This may not be the complete list of references from this article.
- 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]
- 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]