A geometric interpretation for local alignment-free sequence comparison

Journal of Computational Biology

Volumn 20, Issue 7, 2013, Pages 471-485

  Behnam, Ehsan ^a   Waterman, Michael S ^a   Smith, Andrew D ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

algorithms; alignment; dynamic programming; metagenomics

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA SEQUENCE; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84880126573     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0280     Document Type: Article

References (46)

1. Agarwal, P., Edelsbrunner, H., Schwartzkopf, O., et al. 1991. Euclidean MST and bichromic closest pairs. Disc. Comput. Geom. 6, 407-422.
2. Alm, E., Huang, K., and Arkin, A. 2006. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comput. Biol. 2, e143.
3. Altschul, S., Gish, W., Miller, W., et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
4. Altschul, S., Madden, T., Schaffer, A., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
5. Berman, B., Nibu, Y., Pfeiffer, B., et al. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99, 757-762.
6. Buhler, J. 2001. Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics 17, 419-428.
7. Charikar, M. 2002. Similarity estimation techniques from rounding algorithms. In Proceedings of the thiry-fourth annual ACM symposium on theory of computing, 380-388.
8. Dayhoff, M., Schwartz, R., and Orcutt, B. 1978. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure 5, 345-352.
9. Domazet-Lošo, M., and Haubold, B. 2011. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 27, 1466-1472.
10. Dutta, D., Guha, R., Jurs, P., et al. 2006. Scalable partitioning and exploration of chemical spaces using geometric hashing. J. Chem. Inf. Model. 46, 321-333.
11. Forêt, S., Wilson, S., and Burden, C. 2009. Empirical distribution of k-word matches in biological sequences. Pattern Recognition 42, 539-548.
12. Goemans, M, and Williamson, D. 1995. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. Journal of the ACM 42, 1115-1145.
13. Göke, J., Schulz, M., Lasserre, J., et al. 2012. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics 28, 656-663.
14. Haubold, B., Reed, F., and Pfaffelhuber, P. 2011. Alignment-free estimation of nucleotide diversity. Bioinformatics 27, 449-455.
15. Haveliwala, T., Gionis, A., and Indyk, P. 2000. Scalable techniques for clustering the web. In Proceeding of the 3rd intl. workshop on web and databases, 129-134.
16. Indyk, P. 2001. High-dimensional computational geometry. [Ph.D. thesis], Department of Computer Science, Stanford University, Stanford, CA.
17. Indyk, P., and Motwani, R. 1998. Approximate nearest neighbors: Towards removing the curse of dimensionality. In Proceedings of the 30th Annual ACM Symposium on Theory of Computing, 604-613.
18. Johnson, M., Zaretskaya, I., Raytselis, Y., et al. 2008. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5-W9.
19. Kantorovitz, M., Robinson, G., and Sinha, S. 2007. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23, 1249-1255.
20. Karlin, S., and Altschul, S. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. 87, 2264-2268.
21. Kazemian, M., Zhu, Q., Halfon, M., et al. 2011. Improved accuracy of supervised CRM discovery with interpolated markov models and cross-species comparison. Nucleic Acids Res. 39, 9463-9472.
22. Khuller, S., and Matias, Y. 1995. A simple randomized sieve algorithm for the closest-pair problem. Information and Computation 118, 34-37.
23. Lippert, R., Huang, H.Y., and Waterman, M. 2002. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl. Acad. Sci. 100, 13980-13989.
24. Liua, X., Wan, L., Li, J., et al. 2011. New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J. Theor. Biol. 284, 106-116.
25. Mahmood, K., Webb, G., Song, J., et al. 2012. Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acid Res. 40, e44.
26. McDaniel, L., Young, E., Delaney, J., et al. 2010. High frequency of horizontal gene transfer in the oceans. Science 330, 50.
27. Meader, S., Ponting, C., and Lunter, G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res. 20, 1335-1343.
28. Motwani, R., and Raghavan, P. 1995. Randomized algorithms. Cambridge University Press, Cambridge, United Kingdom.
29. Muller, M. 1959. A note on a method for generating points uniformly on n-dimensional spheres. Communications of the Association for Computing Machinery 2, 19-20.
30. Pearson, W., and Lipman, D. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. 85, 2444-2448.
31. Preparata, F., and Shamos, M. 1985. Computational geometry: an introduction. Springer-Verlag, New York.
32. Ravichandran, D., Pantel, P., and Hovy, E. 2005. Randomized algorithms and NLP: using locality sensitive hash function for high speed noun clustering. In Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics, 622-629.
33. Reinert, G., Chew, D., Sun, F., et al. 2009. Alignment-free sequence comparison (I): statistics and power. J. Comp. Biol. 16, 1615-1634.
34. Sims, G., and Kim, S. 2011. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Natl. Acad. Sci. 108, 8329-8334.
35. Sinha, S., and Siggia, E. 2005. Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila. Mol. Biol. Evol. 22, 874-885.
36. Smith, T., and Waterman, M. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
37. Song, K., Ren, J., Zhai, Z., et al. 2012. Alignment-free sequence comparison based on next generation sequencing reads: extended abstract. In RECOMB, 272-285.
38. Taher, L., McGaughey, D., Maragh, S., et al. 2011. Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res. 21, 1139-1149.
39. Tan, P., Steinbach, M., and Kumar, V. 2006. Introduction to data mining (Chapter 8). Addison-Wesley, Boston, MA.
40. Torney, D., Burks, C., Davison, D., et al. 1990. Computation of D2: a measure of sequence dissimilarity. Computers and DNA, 109-125.
41. Ture, F., Elsayed, T., and Lin, J. 2011. No free lunch: brute force vs locality-sensitive hashing for cross-lingual pairwise similarity. In Proceedings of ACM Special Interest Group on Information Retrieval, 943-952.
42. Venkataram, S., and Fay, J. 2010. Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence? Genome Biol Evol. 2, 851-858.
43. Wan, L., Reinert, G., Sun, F., et al. 2010. Alignment-free sequence comparison (II): theoretical power of comparison statistics. J. Comput. Biol. 17, 1467-1490.
44. Waterman, M., and Vingron, M., 1994. Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl. Acad. Sci. 91, 4625-4628.
45. Yao, A. 1982. On constructing minimum spanning trees in k-dimensional spaces and related problems. SIAM J. Comput. 11, 721-736.
46. Zhang, Z., Schaffer, A., Miller, W., et al. 1998. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res. 26, 3986-3990.