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Asymmetric directional mutation pressures in bacteria
Jean R Lobry, Noboru Sueoka
Genome Biol. 2002; 3(10): research0058.1–research0058.14. Published online 2002 September 26.
PMCID:
PMC134625
Abstract Full Text PDF–328K Supplementary Material

Is Cited by the Following 20 Articles in this Archive:

Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations
Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
PLoS One. 2012; 7(4): e34526. Published online 2012 April 3. doi: 10.1371/journal.pone.0034526
PMCID:
PMC3317982
Abstract Full Text PDF–685K Supplementary Material
Measures of Compositional Strand Bias Related to Replication Machinery and its Applications
Kazuharu Arakawa, Masaru Tomita
Curr Genomics. 2012 March; 13(1): 4–15. Published online 2012 March. doi: 10.2174/138920212799034749
PMCID:
PMC3269016
Free in PMC on 2012/09/01
Atypical AT Skew in Firmicute Genomes Results from Selection and Not from Mutation
Catherine A. Charneski, Frank Honti, Josephine M. Bryant, Laurence D. Hurst, Edward J. Feil
PLoS Genet. 2011 September; 7(9): e1002283. Published online 2011 September 15. doi: 10.1371/journal.pgen.1002283
PMCID:
PMC3174206
Abstract Full Text PDF–620K Supplementary Material
Modeling compositional dynamics based on GC and purine contents of protein-coding sequences
Zhang Zhang, Jun Yu
Biol Direct. 2010; 5: 63. Published online 2010 November 8. doi: 10.1186/1745-6150-5-63
PMCID:
PMC2989939
Abstract Full Text PDF–1.2M Supplementary Material
Evolutionary Rates and Gene Dispensability Associate with Replication Timing in the Archaeon Sulfolobus islandicus
Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper
Genome Biol Evol. 2010; 2: 859–869. Published online 2010 October 12. doi: 10.1093/gbe/evq068
PMCID:
PMC3000693
Abstract Full Text PDF–742K
Translational Selection Is Ubiquitous in Prokaryotes
Fran Supek, Nives Škunca, Jelena Repar, Kristian Vlahoviček, Tomislav Šmuc
PLoS Genet. 2010 June; 6(6): e1001004. Published online 2010 June 24. doi: 10.1371/journal.pgen.1001004
PMCID:
PMC2891978
Abstract Full Text PDF–682K Supplementary Material
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index
Kazuharu Arakawa, Haruo Suzuki, Masaru Tomita
BMC Genomics. 2009; 10: 640. Published online 2009 December 30. doi: 10.1186/1471-2164-10-640
PMCID:
PMC2804667
Abstract Full Text PDF–437K Supplementary Material
Hidden Chromosome Symmetry: In Silico Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes
Maria S. Poptsova, Sergei A. Larionov, Eugeny V. Ryadchenko, Sergei D. Rybalko, Ilya A. Zakharov, Alexander Loskutov
PLoS One. 2009; 4(7): e6396. Published online 2009 July 28. doi: 10.1371/journal.pone.0006396
PMCID:
PMC2712679
Abstract Full Text PDF–800K Supplementary Material
A comparative approach to elucidate chloroplast genome replication
Neeraja M Krishnan, Basuthkar J Rao
BMC Genomics. 2009; 10: 237. Published online 2009 May 20. doi: 10.1186/1471-2164-10-237
PMCID:
PMC2695485
Abstract Full Text PDF–1.0M Supplementary Material
CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition
Jesse Zaneveld, Micah Hamady, Noboru Sueoka, Rob Knight
Methods Mol Biol. Author manuscript; available in PMC 2010 October 13.
Published in final edited form as: Methods Mol Biol. 2009; 537: 207–232. doi: 10.1007/978-1-59745-251-9_10
PMCID:
PMC2953947
Abstract Full Text PDF–3.5M
Comparison of methods for estimating the nucleotide substitution matrix
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser, Rob Knight
BMC Bioinformatics. 2008; 9: 511. Published online 2008 December 1. doi: 10.1186/1471-2105-9-511
PMCID:
PMC2655096
Abstract Full Text PDF–415K
Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes
Richard A Morton, Brian R Morton
BMC Genomics. 2007; 8: 369. Published online 2007 October 12. doi: 10.1186/1471-2164-8-369
PMCID:
PMC2099444
Abstract Full Text PDF–1.1M Supplementary Material
Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method
Feng-Biao Guo, Xiu-Juan Yu
BMC Genomics. 2007; 8: 366. Published online 2007 October 10. doi: 10.1186/1471-2164-8-366
PMCID:
PMC2089121
Abstract Full Text PDF–374K
Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes
Chi Chen, Carton W Chen
BMC Genomics. 2007; 8: 286. Published online 2007 August 21. doi: 10.1186/1471-2164-8-286
PMCID:
PMC2031905
Abstract Full Text PDF–1.5M Supplementary Material
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
Micah Hamady, M D Betterton, Rob Knight
BMC Bioinformatics. 2006; 7: 476. Published online 2006 October 26. doi: 10.1186/1471-2105-7-476
PMCID:
PMC1657035
Abstract Full Text PDF–1.0M
Multireplicon genome architecture of Lactobacillus salivarius
Marcus J. Claesson, Yin Li, Sinead Leahy, Carlos Canchaya, Jan Peter van Pijkeren, Ana M. Cerdeño-Tárraga, Julian Parkhill, Sarah Flynn, Gerald C. O’Sullivan, J. Kevin Collins, Des Higgins, Fergus Shanahan, Gerald F. Fitzgerald, Douwe van Sinderen, Paul W. O’Toole
Proc Natl Acad Sci U S A. 2006 April 25; 103(17): 6718–6723. Published online 2006 April 14. doi: 10.1073/pnas.0511060103
PMCID:
PMC1436024
Abstract Full Text PDF–1.0M Supplementary Material
Comparative context analysis of codon pairs on an ORFeome scale
Gabriela Moura, Miguel Pinheiro, Raquel Silva, Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, José L Oliveira, Manuel AS Santos
Genome Biol. 2005; 6(3): R28. Published online 2005 February 15. doi: 10.1186/gb-2005-6-3-r28
PMCID:
PMC1088947
Abstract Full Text PDF–527K
Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics
Alex Mira, Ravindra Pushker, Boris A Legault, David Moreira, Francisco Rodríguez-Valera
BMC Evol Biol. 2004; 4: 50. Published online 2004 November 26. doi: 10.1186/1471-2148-4-50
PMCID:
PMC535925
Abstract Full Text PDF–595K Supplementary Material
Detecting Gradients of Asymmetry in Site-Specific Substitutions in Mitochondrial Genomes
NEERAJA M. KRISHNAN, HERVÈ SELIGMANN, SAMEER Z. RAINA, DAVID D. POLLOCK
DNA Cell Biol. Author manuscript; available in PMC 2010 September 22.
Published in final edited form as: DNA Cell Biol. 2004 October; 23(10): 707–714. doi: 10.1089/1044549042476901
PMCID:
PMC2943950
Abstract Full Text PDF–1.0M
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, Jizhong Zhou
BMC Evol Biol. 2004; 4: 19. Published online 2004 June 28. doi: 10.1186/1471-2148-4-19
PMCID:
PMC476735
Abstract Full Text PDF–2.2M
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