Statistical bioinformatic methods in microbial genome analysis

BioEssays

Volumn 25, Issue 3, 2003, Pages 266-273

  Liò, Pietro ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

BIOINFORMATICS; DNA REPLICATION; GENOME ANALYSIS; MODEL; NONHUMAN; OPERON; PHYLOGENY; REGULATORY MECHANISM; REVIEW; STATISTICAL ANALYSIS;

COMPUTATIONAL BIOLOGY; DATABASES; DNA; GENE TRANSFER TECHNIQUES; GENOME, BACTERIAL; MARKOV CHAINS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PHYLOGENY; RNA; SOFTWARE;

EID: 0037338287     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/bies.10231     Document Type: Review

References (57)

1. Vingron M. Bioinformatics needs to adopt statistical thinking. Bioinformatics 2001;17:389-390.
2. Searls DB. Bioinformatics tools for whole genomes. Annu Rev Genomics Hum Genet 2000;1:251-279.
3. Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL. A probabilistic method: for identifying start codons in bacterial genomes. Bioinformatics 2001;17:1123-1130.
4. Ermolaeva MD, Hanif G Khalak, White O, Smith HO, Salzberg SL. Prediction of Transcription Terminators in Bacterial Genomes. J Mol Biol 2000;301:27-33.
5. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with Glimmer. Nucleic Acids Res. 1999;27:4636-4641.
6. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001;29:2607-2618.
7. Rivas E, Klein RJ, Jones TA, Eddy SR. Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biology 2001;11:1369-1373.
8. Durbin R, Eddy S, Krogh A, Mitchinson G. Markov chains and hidden Markov models in Biological sequence analysis. Cambridge University Press 1998.
9. Baldi P, Brunak S. Bioinformatics the machine learning approach. The MIT Press, 1998.
10. Grosse I, Herzel H, Buldyrev SV, Stanley HE. Species Independence of Mutual Information in Coding and Noncoding DNA. Physical Review E 2000;61:5624-5629.
11. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucleic Acids Res 2001;29:22-28.
12. Karp PD, Riley M, Saier M, Paulsen IT, Paley S, Pellegrini-Toole A. The Ecocyc Database. Nucleic Acids Res 2002;30:56.
13. Ermolaeva MD, White O, Salzberg SL. Prediction of operons in microbial genomes. Nucleic Acids Res 2001;29:1216-1221.
14. Sawyer S. Statistical tests for detecting gene conversion. Mol Biol Evol 1989;6:526-538.
15. Wiuf C, Christensen T, Hein J. A simulation study of the reliability of recombination detection methods. Mol Biol Evol 2001;18:1929-1939.
16. Gu X. Maximum likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 2001;18:453-464.
17. Nekrutenko A, Li WH. Assessment of compositional heterogeneity within and between eukaryotic genomes Genome Res 2000;10:1986-1995.
18. Liò P, Vannucci M. Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics 2000;16:932-940.
19. Churchill GA. Stochastic models for heterogeneous DNA sequences. Bull Math Biol 1989;51:79-94.
20. Nicolas P, Bize L, Muri F, Hoebeke M, Rodolphe F, D Ehrlich S, Prum B, Bessières P. Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Research 2002;30:1418-1426.
21. Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 1995;11:283-290
22. Karlin S, Campbell AM, Mrazek J. Comparative DNA analysis across diverse genomes. Ann Rev Genet 1998;32:185-225.
23. Karlin S. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 2001;9:335-343.
24. Badger JH, Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 1999;16:512-524.
25. Reinert G, Schbath S, Waterman MS. Probabilistic and Statistical properties of words: an overview. J Comput Biol 2000;7:1-46.
26. Schmitt A, Herzel HP. Estimating the entropy of DNA sequences. J Theoret Biol 1997;188:369-377.
27. Lobry JR. Asymmetric substitution patterns in the two strands of bacteria. Mol Biol Evol 1996;13:660-665.
28. McLean MJ, Wolfe KH, Devine KM. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 1998;47:691-696.
29. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Research 1998;26:2286-2290.
30. Mrazek J, Karlin S. Strand compositional asimmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 1998;95:3720-3725.
31. Rocha EP, Danchin A. Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 2001;18:1789-1799.
32. Salzberg SL. Skewed oligomers and origins of replication. Gene 1998;217:57-67.
33. Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biology 2000;1(6): research0011.1-0011.9.
34. Rajewsky N, Socci ND, Zapotocky M, Siggia ED. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res 2002;12:298-308.
35. Schneider TD. Evolution of biological information. Nucleic Acids Res 2000;28:2794-2799.
36. Stormo GD. DNA binding sites: representation and discovery. Bioinformatics 2000;16:16-23.
37. Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999;15:563-577.
38. Bussemaker HJ, Li H, Siggia ED. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci USA 2000;97:10096-10100.
39. Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nature Genet 2001;27:167-171.
40. Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. J Mol Biol 2000;299:907-930.
41. Bolshoy A, Nevo E. Ecologic genomics of DNA:upstream bending in prokaryotic promoters. Genome Res 2000;10:1185-1193.
42. Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, Leibler S, Surette MG, Alon U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 2001;292:2080-2083.
43. Kanehisa M. Post-Genome Informatics. Oxford University Press. 2000.
44. Bray D. Bacterial chemotaxis and the question of gain. Proc Natl Acad Sci USA 2002;99:7-9.
45. James M. Bower Hamid Bolouri Computational Modeling of Genetic and Biochemical Networks. MIT Press 2001.
46. Gilman A, Arkin AP. Genetic Code: Representations and Dynamical Models of Genetic Components and Networks. Annu Rev Genomics Hum Genet 2002 Jun 6.
47. Shen-Orr S, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 2002;31:64-68.
48. Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-art methods for looking into the past Trends Genet 2001;17:262-272.
49. Swofford DL. Phylogenetic inference In: Molecular Systematics. Hillis DM, ed. 1996;407-514, Sinauer Associates.
50. Edwards AWF. Likelihood. 1972; Cambridge University Press.
51. Shoemaker JS, Painter IS, Weir BS. Bayesian statistics in genetics: a guide for the uninitiated. Trends Genet 1999;15:354-358.
52. Warren J. J. Ewens Gregory Grant Gregory R. Grant (2001) Statistical Methods in Bioinformatics: An Introduction Springer-Verlag New York, Incorporated.
53. Anisimova M, Bielawski JP, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 2001;18:1585-1592.
54. Nei M, Gojobori T. Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986;3:418-426.
55. Nielsen RZ. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 1998;148:929-936.
56. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 1997;13:555-556.
57. Ranian Patnaik, Susan Louie, Vesna Gavrilovic, Kim Perry, Willem PC Stemmer, Chris M Ryan, Stephen del Cardayré. Genome shuffling of Lactobacillus for improved acid tolerance. Nature Biotechnol 2002;20:707-712.