Alignment-free sequence comparison (II): Theoretical power of comparison statistics

Journal of Computational Biology

Volumn 17, Issue 11, 2010, Pages 1349-1372

  Wan, Lin ^a   Reinert, Gesine ^b   Sun, Fengzhu ^a,c   Waterman, Michael S ^a,c  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

alignment free; hidden Markov model; motifs; normal approximation; power; sequence alignment; word count statistics

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; MATHEMATICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ALGORITHMS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; MATHEMATICS; MODELS, STATISTICAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 78349292948     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0056     Document Type: Article

References (15)

1. Burden, C. J., Kantorovitz, M. R., and Wilson, S. R. 2006. Approximate word matches between two random sequences. Ann. Appl. Probab. 18:1-21.
2. Forêt, S., Kantorovitz, M. R., and Burden, C. J. 2006. Asymptotic behaviour and optimal word size for exact and approximate word matches between random sequences.. BMC Bioinform. 7: S21.
3. Forêt, S., Wilson, S. R., and Burden, C. J. 2009a. Empirical distribution of k-word matches in biological sequences. Pattern Recogn. 42:539-548.
4. Forêt, S., Wilson, S. R., and Burden, C. J. 2009b. Characterizing the D2 statistic: word matches in biological sequences. Stat. Appl. Genet. Mol. Biol. 8:43.
5. Ivan, A., Halfon, M. S., and Sinha, S. 2008. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol. 9: R22.
6. Kantorovitz, M. R., Booth, H. S., Burden, C. J., and Wilson, S. R. 2007a. Asymptotic behavior of k-word matches between two uniformly distributed sequences. J. Appl. Probab. 44:788-805.
7. Kantorovitz, M. R., Robinson, G. E., and Sinha, S. 2007b. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23: i249-i255.
8. Lippert, R. A., Huang, H. Y., and Waterman, M. S. 2002. Distributional regimes for the number of k-word matches between two random sequences. Proc. Natl. Acad. Sci. USA, 100:13980-13989.
9. Mantegna, R. N., Buldyrev, S. V., Goldberger, A. L., et al. 1994. Linguistic features of noncoding DNA sequences. Phys. Rev. Lett. 73:3169-3172.
10. Novak, S. Y. 2007. A new characterization of the normal law. Stat. Probabil. Lett. 77:95-98.
11. Reinert, G., Chew, D., Sun, F. Z., et al. 2009. Alignment-free sequence comparison (I): Statistics and power. J. Comput. Biol. 16:1615-1634.
12. Rabiner, L. R. 1989. A tutorial on hidden markov models and selected applications in speech recognition. Proc. IEEE 77:257-286.
13. Stormo, G. D. 2000. DNA binding sites: representation and discovery. Bioinformatics 16:16-23.
14. Sandelin, A., Alkema, W., Engström, P., et al. 2004. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32: D91-D94.
15. Zhai, Z. Y., Ku, S. Y., Luan, Y. H., et al. 2010. The power of detecting enriched patterns: an HMM approach. J. Comput. Biol. 17:581-592.