A web site for the computational analysis of yeast regulatory sequences

Yeast

Volumn 16, Issue 2, 2000, Pages 177-187

  Van Helden, J ^a,b   Andre B ^b   Collado Vides, J ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Bioinformatics; Sequence analysis; Transcriptional regulation; Yeast

Indexed keywords

COMPUTER ANALYSIS; COMPUTER PROGRAM; FUNGAL GENETICS; GENE EXPRESSION REGULATION; GENE ISOLATION; INTERNET; NONHUMAN; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES CEREVISIAE;

EID: 0034731822     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9     Document Type: Review

References (13)

1. deRisi JL, Iyer VR, Brown PO. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
2. Durbin R, Eddy S, Krogh A, Mitchion G. 1998. Biological Sequence Analysis - Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press: Cambridge, MA.
3. Ghosh D. 1999. Object-oriented transcription factors database (ooTFD). Nucleic Acids Res 27: 315-317.
4. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG. 1996. Life with 6000 genes. Science 274 (5287): 546, 563-567.
5. Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel AE, Kel OV, Ignatieva EV, Ananko EA, Podkolodnaya OA, Kolpakov FA, Podkolodny NL, Kolchanov NA. 1998. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res 26: 362-367.
6. Hertz GZ, Hartzell GW, Stormo GD. 1990. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 6: 81-92.
7. Hertz GZ, Stormo GD. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 (in press).
8. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. 1993. Detecting subtle signals: a Gibbs sampling strategy for multiple alignment. Science 262: 208-214.
9. Neuwald AF, Liu JS, Lawrence CE. 1995. Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4: 1618-1632.
10. Oshima Y, Ogawa N, Harashima S. 1996. Regulation of phosphatase synthesis in Saccharomyces cerevisiae: a review. Gene 179: 171-177.
11. Schjerling P, Holmberg S. 1996. Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators. Nucleic Acids Res 24: 4599-4607.
12. van Helden J, André B, Collado-Vides J. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281: 827-842.
13. Yada T, Totoki Y, Ishikawa M, Asai K, Nakai K. 1998. Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinformatics 14: 317-325.