Alignment-free phylogeny of whole genomes using underlying subwords

Algorithms for Molecular Biology

Volumn 7, Issue 1, 2012, Pages

  Comin, Matteo ^a   Verzotto, Davide ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

Alignment free algorithms; Pattern discovery; Phylogeny

Indexed keywords

EID: 84870417740     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-34     Document Type: Article

References (35)

1. Wildman D, Uddin M, Opazo JC, Liu G, Lefort V, Guindon S, Gascuel O, Grossman LI, Romero R, Goodman M. Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci USA 2007, 104:14395-14400. 10.1073/pnas.0704342104, 1958817, 17728403.
2. Huynen M, Bork P. Measuring genome evolution. Proc Natl Acad Sci USA 1998, 95:5849-5856. 10.1073/pnas.95.11.5849, 34486, 9600883.
3. Chor B, Horn D, Goldman N, Levy Y, Massingham T. Genomic DNA k-mer spectra: models and modalities. Genome Biol 2009, 10(10):R108. 10.1186/gb-2009-10-10-r108, 2784323, 19814784.
4. Sims GE, Jun SRR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Nat Acad Sci USA 2009, 106(8):2677-2682. 10.1073/pnas.0813249106, 2634796, 19188606.
5. Venter C, et al. The sequence of the human genome. Science 2001, 291:1305-1350.
6. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6:361-375.
7. Ulitsky I, Burstein D, Tuller T, Chor B. The average common substring approach to phylogenomic reconstruction. J Comput Biol 2006, 13(2):336-350. 10.1089/cmb.2006.13.336, 16597244.
8. Sims GE, Jun SR, Wu GA, Kim SH. Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions. Proc Nat Acad Sci USA 2009, 106(40):17077-17082. 10.1073/pnas.0909377106, 2761373, 19805074.
9. Lin J. Divergence measures based on the Shannon entropy. IEEE T Inform Theory 1991, 37:145-151.
10. Apostolico A, Comin M, Parida L. Mining, compressing and classifying with extensible motifs. Algorithms Mol Biol 2006, 1:4. 10.1186/1748-7188-1-4, 1459173, 16722593.
11. Apostolico A, Comin M, Parida L. Motifs in Ziv-Lempel-Welch Clef. Proceedings of IEEE DCC Data Compression Conference 2004, 72-81. IEEE Computer Society.
12. Giancarlo R, Scaturro D, Utro F. Textual data compression in computational biology: a synopsis. Bioinformatics 2009, 25(13):1575-1586. 10.1093/bioinformatics/btp117, 19251772.
13. Iliopoulos C, Mchugh J, Peterlongo P, Pisanti N, Rytter W, Sagot MF. A first approach to finding common motifs with gaps. Int J Foundations Comput Sci 2005, 16(6):1145-1154.
14. Apostolico A, Comin M, Parida L. Conservative extraction of over-represented extensible motifs. Bioinformatics 2005, 21(Suppl 1):i9-i18. 10.1093/bioinformatics/bti1051, 15961503.
15. Apostolico A, Comin M, Parida L. VARUN: discovering extensible motifs under saturation constraints. IEEE/ACM Trans Comput Biol Bioinformatics 2010, 7(4):752-762.
16. Kong SG, Fan WL, Chen HD, Hsu ZT, Zhou N, Zheng B, Lee HC. Inverse symmetry in complete genomes and whole-genome inverse duplication. PLoS ONE 2009, 4(11):e7553. 10.1371/journal.pone.0007553, 2771390, 19898631.
17. Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology 1997, New York, USA: Cambridge University Press.
18. Apostolico A. The myriad virtues of subword trees. Combinatorial Algorithms on Words, A. Apostolico, Z. Galil (Eds.) 1985, 12:85-96.
19. Apostolico A. Maximal words in sequence comparisons based on subword composition. Algorithms and Applications, Volume 6060 of Lecture Notes in Computer Science 2010, 34-44. Berlin: Springer-Verlag, Elomaa T, Mannila H, Orponen P.
20. Apostolico A, Parida L. Incremental paradigms of motif discovery. J Comput Biol 2004, 11:15-25. 10.1089/106652704773416867, 15072686.
21. Comin M, Verzotto D. Classification of protein sequences by means of irredundant patterns. BMC Bioinformatics 2010, 11(Suppl. 1):S16. 3024869, 21172051.
22. Comin M, Verzotto D. The Irredundant Class method for remote homology detection of protein sequences. J Comput Biol 2011, 18(12):1819-1829. [http://dx.doi.org/10.1089/cmb.2010.0171], 10.1089/cmb.2010.0171, 21548811.
23. Apostolico A, Comin M, Parida L. Bridging lossy and lossless compression by motif pattern discovery. Lect Notes Comput Sci 2006, 4123:793-813.
24. Comin M, Parida L. Detection of subtle variations as consensus motifs. Theor Comput Sci 2008, 395(2-3):158-170.
25. Ukkonen E. Maximal and minimal representations of gapped and non-gapped motifs of a string. Theor Comput Sci 2009, 410(43):4341-4349.
26. Comin M, Verzotto D. Comparing, ranking and filtering motifs with character classes: application to biological sequences analysis. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data 2013, chapter 13-chapter 13. Wiley, Elloumi M, Zomaya AY.
27. Cormen TH, Leiserson CE, Rivest RL. Introduction To Algorithms, chap. 9 1990, MIT Press, 178-180.
28. Kopelowitz T, Lewenstein M. Dynamic weighted ancestors. Proceedings of the Eighteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007) 2007, 565-574. Society for Industrial and Applied Mathematics Philadelphia SIAM.
29. Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JSM, Guan Y, Rambaut A. Origins and evolutionary genomics of the 2009 swine-origin H1N1 Influenza A epidemic. Nature. Nature Publishing Group 2009, 459(7250):1122-1125.
30. Shiino T, Okabe N, Yasui Y, Sunagawa T, Ujike M, Obuchi M, Kishida N, Xu H, Takashita E, Anraku A, Ito R, Doi T, Ejima M, Sugawara H, Horikawa H, Yamazaki S, Kato Y, Oguchi A, Fujita N, Odagiri T, Tashiro M, Watanabe H. Molecular Evolutionary Analysis of the Influenza A(H1N1)pdm, May-September, 2009: Temporal and Spatial Spreading Profile of the Viruses in Japan. PLoS ONE 2010, 5(6):e11057. 10.1371/journal.pone.0011057, 2883557, 20548780.
31. Thompson J, Higgins D, Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
32. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
33. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009, 37:D141-D145. 10.1093/nar/gkn879, 2686447, 19004872.
34. Martinsen ES, Perkins SL, Schall JJ. A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches. Mol Phylogenet Evol 2008, 47:261-273. 10.1016/j.ympev.2007.11.012, 18248741.
35. Critchlow D, Pearl D, Qian C. The triples distance for rooted bifurcating phylogenetic trees. Syst Biol 1996, 45(3):323-334.