A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

Bioinformatics

Volumn 17, Issue 12, 2002, Pages 1113-1122

  Thijs, Gert ^a   Lescot, Magali ^a   Marchal, Kathleen ^a   Rombauts, Stephane ^b   De Moor, Bart ^a   Rouzé, Pierre ^b   Moreau, Yves ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC MODEL; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RELIABILITY; SAMPLING; SIMULATION;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 0036137323     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.12.1113     Document Type: Article

References (33)

1. Basic local alignment search tool
2. Unsupervised learning of multiple motifs in biopolymers using Expectation Maximization
3. Gene expression data analysis
4. Regulatory elements and expression profiles
5. The transcriptional program of sporulation in budding yeast
6. Improved microbial gene identification with Glimmer
7. Exploring the metabolic and genetic control of gene expression on a genomic scale
8. Differential gene expression in Arabidopsis monitored using cDNA arrays
9. Mutation of either G-box or I-box sequences profoundly affects expression from the Arabidopsis rbcS-1A promoter
10. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
11. Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies
12. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
13. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
14. Two methods for improving performance of an HMM and their application for gene finding
15. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
16. Bayesian inference on biopolymer models
17. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
18. BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
19. Genomics, gene expression and DNA arrays
20. GeneMark.hmm: New solutions for gene finding
21. Phylogenetic footprinting of transcription factor binding sites in probacterial genomes
22. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
23. Identification and analysis of eukaryotic promoters: Recent computational approaches
24. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
25. PlantCARE, a plant cis-acting regulatory element database
26. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole genome mRNA quantitation
27. EuGene: A eucaryotic gene finder that combines several sources of evidence
28. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridisation
29. A Gibbs sampling method to detect over-represented motifs in upstream regions of co-expressed genes
30. Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals
31. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
32. ANN-SPEC: A method for discovering transcription binding sites with improved specificity
33. Large-scale gene expression data analysis: A new challenge to computational biologist