Exhaustive computation of exact duplications via super and non-nested local maximal repeats

Journal of Bioinformatics and Computational Biology

Volumn 12, Issue 1, 2014, Pages

  Taillefer, Eddy ^a   Miller, Jonathan ^a  

^a OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Genome sequence; length distribution; maximal repeat; overlapping; power law; suffix array

Indexed keywords

ALGORITHM; ARTICLE; DNA SEQUENCE; GENOMICS; METHODOLOGY; NUCLEOTIDE REPEAT;

ALGORITHMS; GENOMICS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

EID: 84894899309     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720013500182     Document Type: Article

References (52)

1. Ohno S, Evolution by Gene Duplication, Springer-Verlag, Berlin, 1970, ISBN 0-04- 575015-7.
2. Ohta T, Further simulation studies on evolution by gene duplication, Evolution 42(2): 375-386, 1988.
3. Taylor JS, Raes J, Duplication and divergence: The evolution of new genes and old ideas, Ann Rev Genet 38:615-643, 2004.
4. Kazazian HH Jr, Mobile elements: Drivers of genome evolution, Science 303(5664): 1626- 1632, 2004.
5. Bailey JA, Eichler EE, Primate segmental duplications: Crucibles of evolution, diversity and disease, Nat Rev Genet 7:552-564, 2006.
6. Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW, Genomewide detection of segmental duplications and potential assembly errors in the human genome sequence, Genome Biol 4(4):R25, 2003.
7. Zhang L, Lu HHS, Chung WY, Yang J, Li WH, Patterns of segmental duplication in the human genome, Mole Biol Evol 22(1):135-141, 2004.
8. Mantegna RN, Buldyrev SV, Goldberger AL, Havlin S, Peng CK, Simons M, Stanley HE, Linguistic features of noncoding DNA sequences, The Amer Phys Soc 73(23):3194-3171, 1994.
9. Csrös M, Noé L, Kucherov G, Reconsidering the significance of genomic word frequencies, TRENDS Genet 23(11):543-546, 2007.
10. Chor B, Horn D, Goldman N, Levy Y, Massingham T, Genomic DNA k-mer spectra: Models and modalities, Genome Biol 10(10):R108.1-10, 2009.
11. Sindi SS, Hunt BR, Yorke JA, Duplication count distributions in DNA sequences, Phys Rev E 78(6):061912(1-11), 2008.
12. Zipf GK, Human Behaviour and the Principle of Least Effort, Addison-Wesley, Cambridge, MA, 1949.
13. Salerno W, Havlak P, Miller J, Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments, Proc Nat Acad Sci 103(35):13121-13125, 2006.
14. Miller J, Colossal ultraconservation and super-colossal ultraconservation, IPSJ SIG Technical Report 2009-BIO-17(7):1-8, 2009.
15. Tran T, Havlak P, Miller J, MicroRNA enrichment among short ̀ultraconserved' sequences in insects, Nucleic Acids Res 34(9):e65, 2006.
16. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, Basic local alignment search tool, J Molec Biol 215(3):403-410, 1990.
17. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res 25(17):3389-3402, 1997.
18. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Miller W, Humanmouse alignments with BLASTZ, Genome Res Meth 13:103-107, 2003.
19. Harris RS, Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University. Available at http://www.bx.psu.edu/rsharris/ rsharris phd thesis 2007.pdf. Software available at http://www.bx.psu.edu/ rsharris/lastz/. Accessed October 2013.
20. Gao K, Miller J, Algebraic distribution of segmental duplication lengths in whole-genome sequence self-alignments, PLoS One 7(6):e18464, 2011.
21. Castelo AT, Martins W, Gao GR, TROLL - Tandem repeat occurrence locator, Bioinformatics 18(4):634-636, 1999.
22. Benson G, Tandem repeats finder: A program to analyze DNA sequences, Nucleic Acids Res 27(2):573-580, 1999.
23. Lefebvre A, Lecroq T, Dauchel H, Alexandre J, FORRepeats: Detects repeats on entire chromosomes and between genomes, Bioinformatics 19(3):319-326, 2003.
24. Becher V, Deymonnaz A, Heiber P, E±cient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome, Bioinformitics 25(14):1746-1753, 2009.
25. Saha S, Bridges S, Magbanua ZV, Peterson DG, Computational approaches and tools used in identification of dispersed repetitive DNA sequences, Tropical Plant Biol 1(1):85- 96, 2008.
26. Saha S, Bridges S, Magbanua ZV, Peterson DG, Empirical comparison of ab initio repeat finding programs, Nucleic Acids Res 36(7):2284-2294, 2008.
27. Delcher AL, Phillippy A, Carlton J, Salzberg SL, Fast algorithms for large-scale genome alignment and comparision, Nucleic Acids Res 30(11):2478-2483, 2002.
28. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R, REPuter: The manifold applications of repeat analysis on a genomic scale, Nucleic Acids Res 29 (22):4633-4642, 2001.
29. Kurtz S, The Vmatch large scale sequence analysis software. Available at http://www. vmatch.de/. Accessed October 2013.
30. Ukkonen E, On-line construction of su±x trees, Algorithmica 14(3):249-260, 1995.
31. Gonnet GH, Baeza-Yates RA, New indices for text: PAT trees and PAT arrays, in Frakes WB, Baeza-Yates RA (eds.)), Information Retrieval: Data Structures and Algorithms, Prentice-Hall, Upper Saddle River, NJ, USA, pp.66-82, 1992.
32. Manber U, Myers G, Su±x arrays: A new method for on-line string searches, SIAM J Comput 22(5):935-948, 1993.
33. Abouelhoda MI, Kurtz S, Ohlebusch E, Replacing su±x trees with enhanced su±x arrays, J Discrete Algorithms 2(1):53-84, 2004.
34. Gusfield D, Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, US, 1997, ISBN 0-521-58519-8.
35. Nicolas J, Rousseau C, Siegel A, Peterlongo P, Tempel S, Valin AS, Mahé F, Modeling local repeats on genomic sequences, Technical Report RR-6802, INRIA, 2008.
36. Luscombe NM, Qian J, Zhang Z, Johnson T, Gerstein M, The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties, Genome Biol 3(8):0040.1-0040.7, 2002.
37. Martindale C, Konopka AK, Oligonucleotide frequencies in DNA follow a Yule distribution, Comput Chem 20(1):35-38, 1996.
38. Gojobori T, Li WH, Graur D, Patterns of nucleotide substitution in pseudogenes and functional genes, J Mole Evol 18(5):360-369, 1982.
39. Koroteev MV, Miller J, Scale-free duplication dynamics: A model for ultraduplication, Phys Rev E 84(6):061919(1-10), 2011.
40. Taillefer E, Miller J, Algebraic length distribution of sequence duplications in whole genomes, Int Conf Natural Computation, Shanghai, China, pp.1454-1460, 2011.
41. Pop M, Salzberg SL, Shumway M, Genome sequence assembly: Algorithms and issues, Computer 35(7):47-54, 2002.
42. Pop M, Genome assembly reborn: Recent computational challenges, Computer 10 (4):354-366, 2009.
43. Narzisi G, Mishra B, Comparing de novo genome assembly: The long and short of it, PloS One 6(4):e19175, 2011.
44. Kasai T, Lee G, Arimura H, Arikawa S, Park K, Linear-time longest-common-prefix computation in su±x arrays and its applications, in Amir A, Landau G (eds.)), Combinat Patt Match, Springer-Verlag, Berlin, Heidelberg, pp.181-192, 2001.
45. Barbour AD, Chryssaphinou O, Compound poisson approximation: A userś guide, Ann Appl Prob 11(3):964-1002, 2001.
46. Lippert RA, Huang H, Waterman MS, Distributional regimes for the number of k-word matches between two random sequences, Proc Nat Acad Sci USA 99(22):13980-13989, 2002.
47. Taillefer E, Miller J, Exhaustive computation of exact sequence duplications in whole genomes via super and local maximal repeats, Int Conf Computer Engineering and Bioinformatics, Cairo, Egypt, pp.22-29, 2011.
48. Kärkkäinen J, Sanders P, Burkhardt S, Simple linear work su±x array construction, J ACM 53(6):918-936, 2006.
49. Nong G, Zhang S, Chan WH, Two e±cient algorithms for linear time su±x array construction, IEEE Trans Comput, IEEE Computer Society Digital Library. IEEE Computer Society, 2010. Available at http://doi. ieeecomputersociety.org/10.1109/TC.2010.188.
50. Mori Y, SAIS: An implementation of the induced sorting algorithm. Available at http:// yuta.256.googlepages.com/sais.
51. Mori Y, Libdivsufsort: A lightweight su±x-sorting library. Available at http://code. google.com/p/libdivsufsort/.
52. Puglisi SJ, Smyth WF, Turpin AH, A taxonomy of su±x array construction algorithms, ACM Comput Surveys 39(2), 2007, article 4.