Biểu diễn áp lực đột biến và áp lực chọn lọc bằng các ma trận PAM

Andersson SG, Zomorodipour A, Andersson JO et al. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature, 396:133–40. Blattner FR, Plunkett G III, Bloch CA et al. 1997. The complete genome sequence of Escherichia coli K-12. Science, 277:1453–62. Dayhoff MO, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in proteins. In Dayhoff MO, ed. Atlas of protein sequence and structure. Volume 5(Suppl 3). Washington: National Biomedical Research Foundation. p 345–52. Frank AC, Lobry JR. 1999. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 238:65–77. Fraser CM, Casjens S, Huang WM et al. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature, 390:580–6. Fraser CM, Norris SJ, Weinstock GM et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science, 281:375–88. Freeman JM, Plasterer TN, Smith TF et al. 1998. Patterns of genome organisation in bacteria. Science, 279:1827. Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science, 185:862–4. Grigoriev A. 1998. Analysing genomes with cumulative skew diagrams. Nucleic Acids Res, 26:2286–90. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci, 8:275–82. Kowalczuk M, Mackiewicz P, Mackiewicz D et al. 2001a. High correlation between the turnover of nucleotides under mutational pressure and the DNA composition [online]. BMC Evol Biol, 1:13. Accessed 17 Dec 2001. URL: http://www.biomedcentral.com/1471-2148/1/13 Kowalczuk M, Mackiewicz P, Szczepanik D et al. 2001b. Multiple base substitution corrections in DNA sequence evolution. Int J Mod Phys C, 12:1043–53. Kowalczuk M, Mackiewicz P, Mackiewicz D et al. 2001c. DNA asymmetry and the replicational mutational pressure. J Appl Genet, 42:553–77. Kunst F, Ogasawara N, Moszer I et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 390:249–56. Lafay B, Lloyd AT, McLean MJ et al. 1999. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res, 27:1642–9. Lobry JR. 1996a. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol, 13:660–5. Lobry JR. 1996b. A simple vectorial representation of DNA sequence for the detection of replication origins in bacteria. Biochimie, 78:323–6. Lobry JR, Sueoka N. 2002. Asymmetric directional mutation pressures in bacteria [online]. Genome Biol, 3:research0058.1–0058.14. Accessed 26 Sep 2002. URL: http://genomebiology.com/2002/3/10/RESEARCH/0058 Mackiewicz P, Gierlik A, Kowalczuk M et al. 1999a. Asymmetry of nucleotide composition of prokaryotic chromosomes. J Appl Genet, 40:1–14. Mackiewicz P, Gierlik A, Kowalczuk M et al. 1999b. How does replication-associated mutational pressure influence amino acid composition of proteins? Genome Res, 9:409–16. Mackiewicz P, Gierlik A, Kowalczuk M et al. 1999c. Mechanisms generating long-range correlation in nucleotide composition of the Borrelia burgdorferi genome. Physica A, 273:103–15. Mackiewicz P, Kowalczuk M, Mackiewicz D et al. 2002. Replication associated mutational pressure generating long-range correlation in DNA. Physica A, 314:646–54. Mackiewicz D, Mackiewicz P, Kowalczuk M et al. 2003a. Rearrangements between differently replicating DNA strands in asymmetric bacterial genomes. Acta Microbiol Pol, 52:245–61. Mackiewicz P, Mackiewicz D, Kowalczuk M et al. 2003b. High divergence rate of sequences located on different DNA strands in closely related bacterial genomes. J Appl Genet, 44:561–84. Mackiewicz P, Szczepanik D, Gierlik A et al. 2001. The differential killing of genes by inversions in prokaryotic genomes. J Mol Evol, 53: 615–21. McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA, 95: 10698–703. McLean MJ, Wolfe KH, Devine KM. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol, 47:691–6. Mrazek J, Karlin S. 1998. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA, 95:3720–5. Nowicka A, Mackiewicz P, Dudkiewicz M et al. 2003. Correlation between mutation pressure, selection pressure and occurrence of amino acids. In: Lecture Notes in Computer Science. Volume 2658. Springer-Verlag. p 650–7. Rocha EP, Danchin A. 2001. Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol, 18:1789–99. Rocha EP, Danchin A. 2003a. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res, 31:6570–7. Rocha EP, Danchin A. 2003b. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet, 34:377–8. Rocha EP, Danchin A, Viari A. 1999. Universal replication biases in bacteria. Mol Microbiol, 32:11–16. Romero H, Zavala A, Musto H. 2000. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res, 28:2084–90. Salzberg SL, Salzberg AJ, Kerlavage AR et al. 1998. Skewed oligomers and origins of replication. Gene, 217:57–67. Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA, 85:2653–7. Sueoka N. 1992. Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol, 34:95–114. Sueoka N. 1995. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol, 40:318–25. Szczepanik D, Mackiewicz P, Kowalczuk M et al. 2001. Evolution rates of genes on leading and lagging DNA strands. J Mol Evol, 52: 426–33. Tillier ERM, Collins RA. 2000a. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol, 50:249–57. Tillier ERM, Collins RA. 2000b. Replication orientation affects the rate and direction of bacterial gene evolution. J Mol Evol, 51:459–63.