Pattern matching through Chaos Game Representation: Bridging numerical and discrete data structures for biological sequence analysis

Algorithms for Molecular Biology

Volumn 7, Issue 1, 2012, Pages

  Vinga, Susana ^a,b   Carvalho, Alexandra M ^c,d   Francisco, Alexandre P ^a,d   Russo, Luís M S ^a,d   Almeida, Jonas S ^e  

^a INESC   (Portugal)

^b UNIVERSIDADE NOVA DE LISBOA   (Portugal)

^c INSTITUTO DE TELECOMUNICAÇÕES   (Portugal)

^d INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^e University of Alabama at Birmingham   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84860351022     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-10     Document Type: Article

References (49)

1. Durbin R, Eddy SR, Krogh A, Mitchison G. Biological sequence analysis: probabalistic models of proteins and nucleic acids 1998, Cambridge, UK New York: Cambridge University Press.
2. Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnology 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
3. Roy A, Raychaudhury C, Nandy A. Novel techniques of graphical representation and analysis of DNA sequences - A review. Journal of Biosciences 1998, 23:55-71.
4. Gusfield D. Algorithms on strings, trees, and sequences: computer science and computational biology 1997, Cambridge England; New York: Cambridge University Press.
5. Navarro G, Mäkinen V. Compressed Full-Text Indexes. ACM Computing Surveys 2007, 39. article 2.
6. Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
7. Li H, Durbin R. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
8. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967. 10.1093/bioinformatics/btp336, 19497933.
9. Fernandes F, da Fonseca PGS, Russo LMS, Oliveira AL, Freitas AT. Efficient alignment of pyrosequencing reads for re-sequencing applications. BMC Bioinformatics 2011, 12:163. 10.1186/1471-2105-12-163, 3118166, 21672185.
10. Jeffrey HJ. Chaos game representation of gene structure. Nucleic Acids Res 1990, 18(8):2163-70. 10.1093/nar/18.8.2163, 330698, 2336393.
11. Arakawa K, Oshita K, Tomita M. A web server for interactive and zoomable Chaos Game Representation images. Source code for biology and medicine 2009, 4:6. 10.1186/1751-0473-4-6, 2753581, 19761591.
12. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 1999, 16(10):1391-9. 10.1093/oxfordjournals.molbev.a026048, 10563018.
13. Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 1995, 11(7):283-90. 10.1016/S0168-9525(00)89076-9, 7482779.
14. Wang YW, Hill K, Singh S, Kari L. The spectrum of genomic signatures: from dinucleotides to chaos game representation. Gene 2005, 346:173-185.
15. Almeida JS, Carrico JA, Maretzek A, Noble PA, Fletcher M. Analysis of genomic sequences by Chaos Game Representation. Bioinformatics 2001, 17(5):429-37. 10.1093/bioinformatics/17.5.429, 11331237.
16. Vinga S, Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19(4):513-23. 10.1093/bioinformatics/btg005, 12611807.
17. Vinga S, Almeida JS. Renyi continuous entropy of DNA sequences. J Theor Biol 2004, 231(3):377-88. 10.1016/j.jtbi.2004.06.030, 15501469.
18. Vinga S, Almeida JS. Local Renyi entropic profiles of DNA sequences. BMC Bioinformatics 2007, 8:393. 10.1186/1471-2105-8-393, 2238722, 17939871.
19. Pandit A, Sinha S. Using genomic signatures for HIV-1 sub-typing. BMC Bioinformatics 2010, 11(Suppl 1):S26. 10.1186/1471-2105-11-S1-S26, 3026373, 20946610.
20. Rasouli M, Rasouli G, Lenz FA, Borrett DS, Verhagen L, Kwan HC. Chaos game representation of human pallidal spike trains. J Biol Phys 2010, 36(2):197-205. 10.1007/s10867-009-9172-x, 2825310, 19688266.
21. Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P. Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Research 2005, 33:e6. 10.1093/nar/gni004, 546175, 15653627.
22. Deschavanne P, Tuffery P. Exploring an alignment free approach for protein classification and structural class prediction. Biochimie 2008, 90(4):615-625. 10.1016/j.biochi.2007.11.004, 18067866.
23. Almeida JS, Vinga S. Computing distribution of scale independent motifs in biological sequences. Algorithms for molecular biology: AMB 2006, 1:18. 10.1186/1748-7188-1-18, 1630425, 17049089.
24. Almeida JS, Vinga S. Universal sequence map (USM) of arbitrary discrete sequences. BMC Bioinformatics 2002, 3:6. 10.1186/1471-2105-3-6, 90187, 11895567.
25. Almeida J, Vinga S. Biological sequences as pictures - a generic two dimensional solution for iterated maps. BMC Bioinformatics 2009, 10:100. 10.1186/1471-2105-10-100, 2678093, 19335894.
26. Buhlmann P, Wyner A. Variable length Markov chains. Annals of Statistics 1999, 27(2):480-513.
27. Tino P, Dorffner G, Schittenkopf C. Understanding state space organization in recurrent neural networks with iterative function systems dynamics. Hybrid Neural Systems, Volume 1778 of Lecture Notes in Artificial Intelligence 2000, 255-269. Wermter S, Sun R, [International Workshop on Hybrid Neural Systems, DENVER, CO, DEC 04-05, 1998].
28. Tino P, Dorffner G. Predicting the future of discrete sequences from fractal representations of the past. Machine Learning 2001, 45(2):187-217.
29. Moreno P, Velez P, Martinez E, Garreta L, Diaz N, Amador S, Tischer I, Gutierrez J, Naik A, Tobar F, Garcia F. The human genome: a multifractal analysis. BMC Genomics 2011, 12:506. 10.1186/1471-2164-12-506, 3277318, 21999602.
30. Ferreirós J. Labyrinth of Thought: A History of Set Theory and Its Role in Modern Mathematics 2007, Birkhäuser Basel.
31. Willard S. General Topology 2004, Dover Publications.
32. Samet H. The quadtree and related hierarchical data-structures. Computing Surveys 1984, 16(2):187-260.
33. Cenac P, Chauvin B, Ginouillac S, Pouyanne N. Digital Search Trees And Chaos Game Representation. ESAIM-Probability and Statistics 2009, 13:15-37.
34. Ukkonen E. On-line construction of suffix trees. Algorithmica 1995, 14(3):249-260.
35. Knuth D, Morris J, Pratt V. Fast pattern matching in strings. SIAM Journal on Computing 1977, 6(2):323-350.
36. Aho A, Corasick M. Efficient string matching: an aid to bibliographic search. Communications of the ACM 1975, 18(6):333-340.
37. Pingoud A, Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Research 2001, 29(18):3705-3727. 10.1093/nar/29.18.3705, 55916, 11557805.
38. Reich NO, Danzitz MJ. Non-additivity of sequence-specific enzyme-DNA interactions in the EcoRI DNA methyltransferase. Nucleic Acids Research 1991, 19(23):6587-6594. 10.1093/nar/19.23.6587, 329224, 1754395.
39. Ussery DW, Wassenaar T, Borini S. Word Frequencies, Repeats, and Repeat-related Structures in Bacterial Genomes. Springer 2008,
40. Kidwell MG. Horizontal transfer of P elements and other short inverted repeat transposons. Genetica 1992, 86(1-3):275-286. 10.1007/BF00133726, 1334912.
41. Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ. Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability. Science 2009, 324(5931):1213-1216. 10.1126/science.1170097, 3132887, 19478187.
42. Baumstark AL, Budowle B, Defenbaugh DA, Smerick JB, Keys KM, Moretti TR. Validation of Short Tandem Repeats (STRs) for Forensic Usage: Performance Testing of Fluorescent Multiplex STR Systems and Analysis of Authentic and Simulated Forensic Samples. Journal of Forensic Sciences 1999, 46(3):647-660.
43. Landau GM, Schmidt JP. An Algorithm for Approximate Tandem Repeats. CPM, Volume 684 of LNCS 1993, 120-133.
44. Landau GM, Vishkin U. Introducing Efficient Parallelism into Approximate String Matching and a New Serial Algorithm. STOC 1986, 220-230. ACM, Hartmanis J.
45. Myers E. An O(ND) Difference Algorithm and Its Variations. Algorithmica 1986, 1(2):251-266.
46. Landau GM, Schmidt JP, Sokol D. An Algorithm for Approximate Tandem Repeats. Journal of Computational Biology 2001, 8:1-18. 10.1089/106652701300099038, 11339903.
47. Karp R, Rabin M. Efficient randomized pattern-matching algorithms. IBM Journal of Research and Development 1987, 31(2):249-260.
48. Cole R. Tight bounds on the complexity of the Boyer-Moore string matching algorithm. Proceedings of the second annual ACM-SIAM symposium on Discrete algorithms 1991, 224-233. SODA '91, Philadelphia, PA, USA: Society for Industrial and Applied Mathematics.
49. Cormen TH, Leiserson CE, Rivest RL, Stein C. Introduction to algorithms 2009, MIT Press.