Expanding yeast knowledge online

Yeast

Volumn 14, Issue 16, 1998, Pages 1453-1469

  Dolinski, Kara ^a   Ball, Catherine A ^a   Chervitz, Stephen A ^a   Dwight, Selina S ^a   Harris, Midori A ^a   Roberts, Shannon ^a   Roe, Taiyun ^a   Cherry, J Michael ^a   Botstein, David ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Munich information center for protein sequences; Saccharomyces genome database; World wide web; Yeast protein database

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN;

AMINO ACID SEQUENCE; CANDIDA ALBICANS; DATA BASE; FUNGAL GENETICS; INFORMATION SERVICE; INTERNET; NONHUMAN; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; YEAST;

AMINO ACID SEQUENCE; BASE SEQUENCE; DATABASES, BIBLIOGRAPHIC; DATABASES, FACTUAL; FUNGAL PROTEINS; GENOME, FUNGAL; INTERNET; YEASTS;

CANDIDA ALBICANS; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

EID: 0032431252     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0061(199812)14:16<1453::AID-YEA348>3.0.CO;2-G     Document Type: Review

References (33)

1. Abola, E. E., Sussmann, J. L., Prilusky, J. and Manning, N. O. (1997). Protein Data Bank archives of three-dimensional macromolecular structures. Meth. Enz. 277, 556-571.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
3. Bairoch, A. and Apweiler, R. (1997). The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucl. Acids Res. 25, 31-36.
4. Bairoch, A., Bucher, P. and Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucl. Acids Res. 25, 217-221.
5. Burns, N., Grimwade, B., Ross-Macdonald, P. B., Choi, E.-Y., Finberg, K., Roeder, G. S. and Snyder, M. (1996). Large-scale characterization of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8, 1087-1105.
6. Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S. and Botstein, D. (1998). SGD: Saccharomyces Genome Database Nucl. Acids Res. 26, 73-79.
7. Cn3D: http://www.ncbi.nlm.nih.gov/Structure/cn3d.html
8. DeRisi, J. L., Iyer, V. R. and Brown, P. O. (1997). Exploring the metabolic and genetic control on a genomic scale. Science 278, 680-686.
9. Frishman, D. and Mewes, H. W. (1997). PEDAN Tic genomic analysis. Trends Genet. 13, 415-416.
10. GenBank: http://www.ncbi.nlm.nih.gov/Web/Genbank/
11. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M. et al. (1996). Life with 6000 genes. Science 274, 546.
12. Grigoriev, A. (1997). Genomes with a view. Trends Genet. 13, 499.
13. Henikoff, J. G. and Henikoff, S. (1996). Blocks database and its applications. Meth. Enz. 266, 88-105.
14. Hodges, P. E., Payne, W. E. and Garrels, J. I. (1998). The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae. Nucl. Acids Res. 26, 68-72.
15. Mewes, H. W., Hani, J., Pfeiffer, F. and Frishman, D. (1998). MIPS: a database for protein sequences and complete genomes. Nucl. Acids Res. 26, 33-37.
16. Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
17. NCBI: http://www.ncbi.nlm.nih.gov/
18. Pearson, W. R. (1991). Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635-650.
19. Pearson, W. R. and Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444-2448.
20. Pedant: http://pedant.mips.biochem.mpg.de/
21. PileUp: part of the Wisconsin Package, Genetics Computer Group (GCG): http://www.gcg.com
22. PIR: http://www-nbrf.georgetown.edu/pir/
23. Protein Database (PDB): http://www.pdb.bnl.gov/
24. PubMed: http://www.ncbi.nlm.nih.gov/PubMed/
25. RasMol: http://www.umass.edu/microbio/rasmol
26. Sacch3D: http://genome-www.stanford.edu/Sacch 3D/
27. Scharf, M., Schneider, R., Casari, G., Bork, P., Valencia, A., Ouzounis, C. and Sander, C. (1994). GeneQuiz: a workbench for sequence analysis. In Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (Eds), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 348-353.
28. Sharp, P. and Li, W. H. (1987). The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucl. Acids Res. 15, 1281-1295.
29. Smith, T. F. and Waterman, M. S. (1981). Identification of common molecular subsequences. J. Molec. Biol. 147, 195-197.
30. Swiss-Prot: http://www.expasy.ch/sprot/
31. Tatusov, R. L., Koonin, E. V. and Lipman, D. J. (1997). A genomic perspective on protein families. Science 278, 631-637.
32. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E. Jr, Hieter, P., Vogelstein, B. and Kinzler, K. W. (1997). Characterization of the yeast transcriptome. Cell 88, 243-251.
33. Wolfe, K. H. and Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.