Noise-reduction filtering for accurate detection of replication termini in bacterial genomes

FEBS Letters

Volumn 581, Issue 2, 2007, Pages 253-258

  Arakawa, Kazuharu ^a   Saito, Rintaro ^a   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Fast Fourier transform; GC skew; Horizontally transferred genes; Origin of replication; Polarization of chromosome

Indexed keywords

NUCLEOTIDE;

ACCURACY; ANALYTIC METHOD; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; COMPUTER MODEL; CONTROLLED STUDY; DNA REPLICATION ORIGIN; FOURIER TRANSFORMATION; GC RICH SEQUENCE; GC SKEW; GENE FUNCTION; GENE REPLICATION; GENE SEQUENCE; GENOME ANALYSIS; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MUTATIONAL ANALYSIS; NOISE REDUCTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTIVE VALIDITY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; TECHNIQUE;

BACTERIA; COMPUTATIONAL BIOLOGY; DNA REPLICATION; FOURIER ANALYSIS; GENOME, BACTERIAL; REPLICATION ORIGIN;

BACTERIA (MICROORGANISMS);

EID: 33846200467     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.12.021     Document Type: Article

References (42)

1. Lobry J.R., and Louarn J.M. Polarisation of prokaryotic chromosomes. Curr. Opin. Microbiol. 6 (2003) 101-108
2. Rocha E.P. The replication-related organization of bacterial genomes. Microbiology 150 (2004) 1609-1627
3. Lobry J.R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol. 13 (1996) 660-665
4. Mrazek J., and Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95 (1998) 3720-3725
5. Rocha E.P. Order and disorder in bacterial genomes. Curr. Opin. Microbiol. 7 (2004) 519-527
6. Lobry J.R., and Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol. 3 (2002) RESEARCH0058
7. McLean M.J., Wolfe K.H., and Devine K.M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47 (1998) 691-696
8. Kowalczuk M., Mackiewicz P., Mackiewicz D., Nowicka A., Dudkiewicz M., Dudek M.R., and Cebrat S. DNA asymmetry and the replicational mutational pressure. J. Appl. Genet. 42 (2001) 553-577
9. Fijalkowska I.J., Jonczyk P., Tkaczyk M.M., Bialoskorska M., and Schaaper R.M. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. USA 95 (1998) 10020-10025
10. Frank A.C., and Lobry J.R. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238 (1999) 65-77
11. Tillier E.R., and Collins R.A. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J. Mol. Evol. 50 (2000) 249-257
12. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26 (1998) 2286-2290
13. Guo F.B., Ou H.Y., and Zhang C.T. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 31 (2003) 1780-1789
14. Zhang C.T., Zhang R., and Ou H.Y. The Z curve database: a graphic representation of genome sequences. Bioinformatics 19 (2003) 593-599
15. Freeman J.M., Plasterer T.N., Smith T.F., and Mohr S.C. Patterns of genome organization in bacteria. Science 279 (1998) 1827a
16. Salzberg S.L., Salzberg A.J., Kerlavage A.R., and Tomb J.F. Skewed oligomers and origins of replication. Gene 217 (1998) 57-67
17. Frank A.C., and Lobry J.R. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16 (2000) 560-561
18. Zawilak A., Cebrat S., Mackiewicz P., Krol-Hulewicz A., Jakimowicz D., Messer W., Gosciniak G., and Zakrzewska-Czerwinska J. Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA. Nucleic Acids Res. 29 (2001) 2251-2259
19. Song J., Ware A., and Liu S.L. Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics 4 (2003) 17
20. Kaguni J.M. Escherichia coli DnaA protein: the replication initiator. Mol. Cells 7 (1997) 145-157
21. Mackiewicz P., Zakrzewska-Czerwinska J., Zawilak A., Dudek M.R., and Cebrat S. Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res. 32 (2004) 3781-3791
22. Capiaux H., Cornet F., Corre J., Guijo M.I., Perals K., Rebollo J.E., and Louarn J.M. Polarization of the Escherichia coli chromosome. A view from the terminus. Biochimie 83 (2001) 161-170
23. Perals K., Capiaux H., Vincourt J.B., Louarn J.M., Sherratt D.J., and Cornet F. Interplay between recombination, cell division and chromosome structure during chromosome dimer resolution in Escherichia coli. Mol. Microbiol. 39 (2001) 904-913
24. Perals K., Cornet F., Merlet Y., Delon I., and Louarn J.M. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36 (2000) 33-43
25. Levy O., Ptacin J.L., Pease P.J., Gore J., Eisen M.B., Bustamante C., and Cozzarelli N.R. Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc. Natl. Acad. Sci. USA 102 (2005) 17618-17623
26. Pease P.J., Levy O., Cost G.J., Gore J., Ptacin J.L., Sherratt D., Bustamante C., and Cozzarelli N.R. Sequence-directed DNA translocation by purified FtsK. Science 307 (2005) 586-590
27. Hendrickson H., and Lawrence J.G. Selection for chromosome architecture in bacteria. J. Mol. Evol. 62 (2006) 615-629
28. Dodin G., Vandergheynst P., Levoir P., Cordier C., and Marcourt L. Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences. J. Theor. Biol. 206 (2000) 323-326
29. Katoh K., Misawa K., Kuma K., and Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 (2002) 3059-3066
30. Yin C., and Yau S.S. A Fourier characteristic of coding sequences: origins and a non-Fourier approximation. J. Comput. Biol. 12 (2005) 1153-1165
31. Arakawa K., Mori K., Ikeda K., Matsuzaki T., Kobayashi Y., and Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19 (2003) 305-306
32. Arakawa K., and Tomita M. G-language system as a platform for large-scale analysis of high-throughput omics data. J. Pesticide Sci. 31 (2006) 282-288
33. Garcia-Vallve S., Guzman E., Montero M.A., and Romeu A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31 (2003) 187-189
34. Sharp P.M., and Li W.H. The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15 (1987) 1281-1295
35. Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
36. Jensen R.B. Analysis of the terminus region of the Caulobacter crescentus chromosome and identification of the dif site. J. Bacteriol. 188 (2006) 6016-6019
37. Myllykallio H., and Forterre P. Mapping of a chromosome replication origin in an archaeon: response. Trends Microbiol. 8 (2000) 537-539
38. Bernander R., and Skarstad K. Mapping of a chromosome replication origin in an archaeon. Trends Microbiol. 8 (2000) 535-537
39. Lopez P., Philippe H., Myllykallio H., and Forterre P. Identification of putative chromosomal origins of replication in Archaea. Mol. Microbiol. 32 (1999) 883-886
40. Grabowski B., and Kelman Z. Archeal DNA replication: eukaryal proteins in a bacterial context. Annu. Rev. Microbiol. 57 (2003) 487-516
41. Moszer I., Glaser P., and Danchin A. Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12. Biochimie 73 (1991) 1361-1374
42. Tillier E.R., and Collins R.A. Genome rearrangement by replication-directed translocation. Nat. Genet. 26 (2000) 195-197