Mining genome databases to identify and understand new gene regulatory systems

Current Opinion in Microbiology

Volumn 5, Issue 2, 2002, Pages 149-153

  Stormo, Gary D ^a   Tan, Kai ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; COMPARATIVE GENE MAPPING; DATA BASE; EVOLUTION; GENE CONTROL; MATHEMATICAL COMPUTING; MOLECULAR INTERACTION; REVIEW; TRANSCRIPTION REGULATION;

BACTERIA (MICROORGANISMS);

EID: 0036220597     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(02)00309-0     Document Type: Review

References (29)

1. Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
2. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
3. RegulonDB(version 3.0): Transcription regulation and operon organization in Escherichia coli
4. Database resources of the National Center for Biotechnology information
5. The comprehensive microbial resource
6. WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction
7. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
8. The use of gene clusters to infer functional coupling
9. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models
10. Operons in Escherichia coli: Genomic analyses and predictions
11. Prediction of operons in microbial genomes
12. A probabilistic learning approach to whole-genome operon prediction
13. DNA binding sites: Representation and discovery
14. Identifying protein-binding sites from unaligned DNA fragments
15. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
16. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
17. Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments
18. Fitting a mixture model by expectation maximization to discover motifs in biopolymers
19. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
20. Expression monitoring by hybridization to high-density oligonucleotide arrays
21. Exploring the metabolic and genetic control of gene expression on a genomic scale
22. Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes
23. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach
24. A comparative genomics approach to prediction of new members of regulons
25. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
26. Predicting regulons and their cis-regulatory motifs by comparative genomics
27. Detecting protein function and protein-protein interactions from genome sequences
28. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
29. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes