GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

Nucleic Acids Research

Volumn 29, Issue 12, 2001, Pages 2607-2618

  Besemer, John ^a   Lomsadze, Alexandre ^a,b   Borodovsky, Mark ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Gene Probe Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; RIBOSOME RNA;

ACCURACY; ALGORITHM; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE SEQUENCE; GENETIC CODE; GENETIC REGULATION; GENETIC TRANSCRIPTION; NONHUMAN; OPEN READING FRAME; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; RNA TRANSLATION; TRAINING;

ESCHERICHIA COLI;

EID: 0035875343     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.12.2607     Document Type: Article

References (47)

1. Recognition of protein coding regions in DNA sequences
2. The codon preference plot: Graphic analysis of protein coding sequences and prediction of gene expression
3. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes
4. Statistical patterns in primary structures of functional regions in the in E. coli genome: III. Computer recognition of coding regions
5. GeneMark: Parallel gene recognition for both DNA strands
6. Microbial gene identification using interpolated Markov models
7. Improved microbial gene identification with GLIMMER
8. A hidden Markov model that finds genes in E. coli DNA
9. GeneMark.hmm: New solutions for gene finding
10. How to interpret an anonymous bacterial genome: Machine learning approach to gene identification
11. Self-identification of protein-coding regions in microbial genomes
12. On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
13. Heuristic approach to deriving models for gene finding
14. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes
15. Finding prokaryotic genes by the 'frame-by-frame' algorithm: Targeting gene starts and overlapping genes
16. Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models
17. Deriving ribosomal binding site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction
18. Initiation of translation in prokaryotes and eukaryotes
19. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
20. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
21. Linguistics of nucleotides sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words
22. Methods for discovering novel motifs in nucleic acid sequences
23. Identification of consensus patterns in unaligned DNA sequences known to be functionally related
24. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
25. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
26. Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Lrp regulon
27. The value of prior knowledge in discovering motifs with MEME
28. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
29. Bacterial start site prediction
30. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
31. Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C
32. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
33. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
34. The complete genome sequence of Escherichia coli K-12
35. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
36. The complete genome sequence of the gastric pathogen Helicobacter pylori
37. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics
38. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
39. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
40. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions
41. Comparing the predicted and observed properties of proteins encoded in the genome of Escherchia coli K-12
42. Sequence logos: A new way to display consensus sequences
43. Basic local alignment search tool
44. Transcription in archaea
45. Archaea: Narrowing the gap between prokaryotes and eukaryotes
46. Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus
47. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs