Distribution patterns of over-represented k-mers in non-coding yeast DNA

Bioinformatics

Volumn 18, Issue 4, 2002, Pages 513-528

  Hampson, Steven ^a   Kibler, Dennis ^a   Baldi, Pierre ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Department of Integrative Physiology and Neurobiology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; FUNGAL DNA; GENOMIC DNA; GUANINE; THYMINE; TRANSCRIPTION FACTOR;

ARTICLE; BASE MISPAIRING; BINDING SITE; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA MICROARRAY; DNA STRUCTURE; GENE CLUSTER; GENE CONTROL; GENE FUNCTION; GENE LOCATION; GENE POOL; GENE STRUCTURE; GENETIC ASSOCIATION; INFORMATION PROCESSING; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; RANDOMIZATION; SEQUENCE HOMOLOGY; STATISTICAL MODEL; STRUCTURE ANALYSIS; YEAST; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; GENOME; METHODOLOGY; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PROTEIN MOTIF; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICS;

AMINO ACID MOTIFS; BASE SEQUENCE; CLUSTER ANALYSIS; CONSERVED SEQUENCE; DATABASES, NUCLEIC ACID; GENE EXPRESSION REGULATION; GENOME, FUNGAL; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; YEASTS;

EID: 0035999971     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.4.513     Document Type: Article

References (36)

1. Unsupervised learning of multiple motifs in biopolymers using expectation maximization
2. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths
3. Structural basis for triplet repreat disorders: A computational analysis
4. Predicting gene regulatory elements in silico on a genomic scale
5. Knowledge-based analysis of microarray gene expression data by using support vector machines
6. Sequence-dependent bending propensity of DNA as revealed by DNase I: Parameters for trinucleotides
7. Over- and under-representation of short oligonucleotides in DNA sequences
8. Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
9. Matrix search 1.0: A computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
10. Exploring the metabolic and genetic control of gene expression on a genomic scale
11. Cluster analysis and display of genome-wide expression patterns
12. Localized DNA flexibility contributes to target site selection by DNA-bending proteins
13. Analysis of yeast's ORFs upstream regions by parallel processing, microarrays, and computational methods
14. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
15. A concise guide to cDNA microarray analysis
16. Combinatorial motif analysis and hypothesis generation on a genomic scale
17. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
18. Poly (dA: dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
19. Compositional differences within and between eukaryotic genomes
20. Learning weight matrices for identifying regulatory elements
21. Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence
22. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
23. Global gene expression profiling in Escherichia coli K12: Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework
24. The structure of an oligo(dA)-oligo(dT) tract and its biological implications
25. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
26. Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor
27. Computational Molecular Biology. An Algorithmic Approach
28. Combinatorial approaches to finding subtle signals in DNA sequences
29. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae
30. DNA bending is an important component of site-specific recognition by the TATA binding protein
31. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
32. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
33. Genome-wide expression monitoring in Saccharomyces cerevisiae
34. Molecular evidence for an ancient duplication of the entire yeast genome
35. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter