Estimating mutation distances from unaligned genomes

Journal of Computational Biology

Volumn 16, Issue 10, 2009, Pages 1487-1500

  Haubold, Bernhard ^a   Pfaffelhuber, Peter ^b   Domazet Lošo, Mirjana ^a,c   Wiehe, Thomas ^d  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

^c UNIVERSITY OF ZAGREB   (Croatia)

^d UNIVERSITY OF COLOGNE   (Germany)

Author keywords

Alignment free distance; Genome comparison; Number of substitutions; Shortest unique substring; Suffix tree

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; DNA SEQUENCE; DROSOPHILA; ENTROPY; GENE CLUSTER; GENE MUTATION; MATHEMATICAL GENETICS; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SIMULATION; STREPTOCOCCUS AGALACTIAE;

ALGORITHMS; ANIMALS; CLUSTER ANALYSIS; DROSOPHILA; GENOME; HUMANS; MODELS, GENETIC; MUTATION; PHYLOGENY; SEQUENCE ALIGNMENT; STREPTOCOCCUS AGALACTIAE;

PRIMATES; STREPTOCOCCUS AGALACTIAE;

EID: 70349789710     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0106     Document Type: Article

References (36)

1. Aanensen, D., and Spratt, B. 2005. The multilocus sequence typing network: mlst.net. Nucleic Acids Res. 33, W728-W733.
2. Abouelhoda, M.I., Kurtz, S., and Ohlebusch, E. 2002. The enhanced suffix array and its applications to genome analysis. In Proc. 2nd Workshop Alg. Bioinform., 449-463. Lecture Notes in Computer Science 2452, Springer-Verlag.
3. Adam, Z., and Sankoff, D. 2008. The ABCs of MGR with DCJ. Evol. Bioinform. 4, 69-74.
4. Archibald, J.D. 2008. Edward Hitchcock's pre-Darwinian (1840) "tree of life." J. History Biol. DOI 10.1007=s10739- 008-9163-y.
5. Blaisdell, B.E. 1986. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Nat. Acad. Sci. USA 83, 5155-5159.
6. Bray, N., and Pachter, L. 2004. MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693-699.
7. Cover, T.M., and Thomas, J.A. 2006. Elements of Information Theory, 2nd ed. Wiley, Hoboken, NJ.
8. Darwin, C. 1859. On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life [1985 edition]. Penguin, London.
9. Dewey, C., and Pachter, L. 2006. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum. Mol. Genet. 15 (spec. no. 1), R51-R56.
10. Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
11. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
12. Felsenstein, J. 2005. PHYLIP (phylogeny interference package), version 3.6.
13. Gascuel, O. 1997. BIONJ: an improved version of the nj algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685-695.
14. Hartl, D.L., and Clark, A.G. 1997. Principles of Population Genetics, 3rd ed. Sinauer, Sunderland, MA.
15. Haubold, B., Domazet-Loso, M., and Wiehe, T. 2008. An alignment-free distance measure for closely related genomes. Lect. Notes Bioinform. 5267, 87-99.
16. Haubold, B., Pierstorff, N., Möller, F., et al. 2005. Genome comparison without alignment using shortest unique substrings. BMC Bioinform. 6, 123.
17. Haubold, B., and Wiehe, T. 2006. How repetitive are genomes? BMC Bioinform. 7, 541.
18. Henz, S., Huson, D., Auch, A., et al. 2005. Whole-genome prokaryotic phylogeny. Bioinformatics 21, 2329-2335.
19. Huson, D.H., and Steel, M. 2004. Phylogenetic trees based on gene content. Bioinformatics 20, 2044-2049.
20. Jukes, T.H., and Cantor, C.R. 1969. Evolution of protein molecules, 21-132. In Munro, H.N., ed., Mammalian Protein Metabolism, Volume 3, Academic Press, New York.
21. Kauffman, S.A. 1993. The Origin of Order. Oxford University Press, Oxford.
22. Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol., Evol. 11, 459-468.
23. Larkin, M., Blackshields, G., Brown, N., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.
24. Lunter, G., Ponting, C.P., and Hein, J. 2006. Genome-wide identification of human functional DNA using a neutral indel model. PLOS Comput. Biol. 2, 2-12.
25. Manzini, G., and Ferragina, P. 2002. Engineering a lightweight suffix array construction algorithm. Proc. 10th Annu. Eur. Symp. Algorithms (ESA '02) 698-710.
26. Pride, D.T., Meinersmann, R.J., and Wassenaar, T.M. 2003. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13, 145-158.
27. Puglisi, S.J., Smyth, W.F., and Turpin, A. H. 2007. A taxonomy of suffix array construction algorithms. ACM Comput. Surv. 39, 4.
28. Robinson, D.F., and Foulds, L.R. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 514-525.
29. Tettelin, H., Masignani, V., Cieslewicz, M., et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome." Proc. Natl. Acad. Sci. USA 102, 13950-13955.
30. Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218.
31. Ulitsky, I., Burstein, D., Tuller, T., et al. 2006. The average common substring approach to phylogenomic reconstruction. J. Comput. Biol 13, 336-350.
32. Vinga, S., and Almeida, J. 2003. Alignment-free sequence comparison-a review. Bioinformatics 19, 513-523.
33. Waterman, M.S. 1995. Introduction to Computational Biology; Maps, Sequences and Genomes. Chapman & Hall=CRC, London.
34. Yang, K., and Zhang, L. 2008. Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Res. 36, e33.
35. Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, New York.
36. Zuckerkandl, E., and Pauling, L. 1965. Molecules as documents of evolutionary history. J. Theoret. Biol. 8, 357-366.