Effective p-value computations using Finite Markov Chain Imbedding (FMCI): Application to local score and to pattern statistics

Algorithms for Molecular Biology

Volumn 1, Issue 1, 2006, Pages

  Nuel, Grégory ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34248358126     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-1-5     Document Type: Article

References (18)

1. Altschul SF Gish W Local alignment statistics Methods in Enzymology Academic Press, London Doolittle RF 1996 266 460-480 8743700
2. Altschul SF Bundschuh R Olsen R Hwa T The estimation of statistical parameters for local score alignment score distributions Nucleic Acids Research 2001 29 2 351-361 29669 11139604 10.1093/nar/29.2.351
3. Bapat RB Raghavan TES Nonegative matrices and applications Cambridge University Press 1997
4. Chothia C The Nature of the accessible and buried surfaces in proteins J Mol Biol 1976 105 1-14 10.1016/0022-2836(76)90191-1 994183
5. Fu JC Koutras MV Distribution theory of runs: A Markov chain approach J Amer Statist Assoc 1994 89 1050-1058 10.2307/2290933
6. Fu JC Distribution theory of runs and patterns associated with a sequence of multi-state trials Statistica Sinica 1996 6 4 957-974
7. Fu JC Lou WYW Distribution Theory of Runs and Patterns and Its Applications: A Finite Markov Chain Approach World Scientific, Singapore 2003
8. Hopcroft JE Motwani R Ullman JD Introduction to Automata Theory, Languages, and Computation (second edition) Addison-Wesley 2001
9. Karlin S Altschul SF Methods for assessing the statistical significance of molecular sequence features by using general Proc Nat Acad Sci USA 1990 87 2264-2268 53667 2315319 10.1073/pnas.87.6.2264
10. Kyte J Doolittle RF A simple method for displaying the hydropathic character of a protein J Mol Biol 1982 157 1 105-132 10.1016/ 0022-2836(82)90515-0 7108955
11. Lou WYW On runs and longest run tests: A method of nite Markov chain imbedding J Am Statist Assoc 1996 91 436 1595-1601 10.2307/2291585
12. Mercier S Daudin J-J Exact Distribution for the Local Score of One i.i.d. Random Sequence J Comp Bio 2001 8 4 373-380 10.1089/ 106652701752236197
13. Mercier S Hassenforder C Exact distribution for the local score of a Markov chain C R Acad Sci Paris 2003 336 10 863-868
14. Nuel G LD-SPatt: Large Deviations Statististic for Pattern on Markov chains J Comp Biol 2004 11 6 1023-1033 10.1089/cmb.2004.11.1023
15. Nuel G S-SPatt: Simple Statististic for Pattern on Markov chains Bioinformatics 2005 21 13 3051-3052 10.1093/bioinformatics/bti451 15840704
16. Press WH Teukolsky SA Vetterling WT Flannery BP Numerical recipes in C Cambridge University Press 1992
17. Robin S Daudin JJ Exact distribution of word occurrences in a random sequence of letters J App Prob 1999 36 179-193 10.1239/jap/1032374240
18. Robin S Daudin J-J Richard H Sagot M-F Schbath S Occurrence probability of structured motifs in random sequences J Comp Biol 2002 9 761-773 10.1089/10665270260518254