Probabilistic arithmetic automata and their application to pattern matching statistics

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5029 LNCS, Issue , 2008, Pages 95-106

  Marschall, Tobias ^a   Rahmann, Sven ^a  

^a TU DORTMUND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; AMINO ACIDS; BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; BIOINFORMATICS; CALCULATIONS; DATABASE SYSTEMS; DIGITAL ARITHMETIC; HEALTH; ORGANIC ACIDS; PATTERN MATCHING; PHASE MODULATION; PROBABILITY; STATISTICAL METHODS; STATISTICS; TRANSCRIPTION FACTORS; TRANSLATION (LANGUAGES);

(SEMI)AUTOMATA; AMINO ACID MOTIFS; BINDING AFFINITIES; COMPUTATIONAL BIOLOGY; GENERIC MANNER; HEIDELBERG (CO); MATCHING STATISTICS; PHYSICAL MODEL (PM); PROBABILISTIC ARITHMETIC; PROSITE; SPRINGER (CO); TRANSCRIPTION FACTOR BINDING SITE (TFBS);

PROBABILITY DISTRIBUTIONS;

EID: 45849126471     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-69068-9_11     Document Type: Conference Paper

References (19)

1. Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., LangendijkGenevaux, P., Pagni, M., Sigrist, C.: The PROSITE database. Nucleic Acids Research 34(S1), D227-230 (2006)
2. Lothaire, M.: Applied Combinatorics on Words (Encyclopedia of Mathematics and its Applications). Cambridge University Press, Cambridge (2005)
3. Reinert, G., Schbath, S., Waterman, M.S.: Probabilistic and statistical properties of words: An overview. Journal of Computational Biology 7(1-2), 1-46 (2000)
4. Régnier, M.: A unifed approach to word occurrence probabilities. Discrete Applied Mathematics 104, 259-280 (2000)
5. Nicodème, P., Salvy, B., Flajolet, P.: Motif statistics. Theoretical Computer Science 287, 593-617 (2002)
6. Lladser, M., Betterton, M.D., Knight, R.: Multiple pattern matching: A Markov chain approach. Journal of Mathematical Biology 56(1-2), 51-92 (2008)
7. Kaltenbach, H.M., Böcker, S., Rahmann, S.: Markov additive chains and applications to fragment statistics for peptide mass fingerprinting. In: Ideker, T., Bafna, V. (eds.) Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics. LNCS (LNBI), vol. 4532, pp. 29-41. Springer, Heidelberg (2007)
8. Zhang, J., Jiang, B., Li, M., Tromp, J., Zhang, X., Zhang, M.Q.: Computing exact p-values for DNA motifs. Bioinformatics 23(5), 531-537 (2007)
9. Stoelinga, M.: An introduction to probabilistic automata. In: Rozenberg, G. (ed.) EATCS bulletin, vol. 78 (2002)
10. Navarro, G., Raffinot, M.: Flexible pattern matching in strings. Cambridge University Press, Cambridge (2002)
11. Hopcroft, J.: An ralogn algorithm for minimizing the states in a finite automaton. In: Kohavi, Z., Paz, A. (eds.) The theory of machines and computations, pp. 189-196. Academic Press, New York (1971)
12. Knuutila, T.: Re-describing an algorithm by Hopcroft. Theoretical Computer Science 250, 333-363 (2001)
13. Aho, A.V., Corasick, M. J.: Efficient string matching: an aid to bibliographic search. Communications of the ACM 18(6), 333-340 (1975)
14. Dori, S., Landau, G.M.: Construction of Aho Corasick automaton in linear time for integer alphabets. Information Processing Letters 98(2), 66-72 (2006)
15. Stormo, G.D.: DNA binding sites: representation and discovery. Bioinformatics 16(1), 16-23 (2000)
16. Pape, U.J., Grossmann, S., Hammer, S., Sperling, S., Vingron, M.: A new statistical model to select target sequences bound by transcription factors. Genome Informatics 17(1), 134-140 (2006)
17. Sandelin, A., Alkema, W., Engström, P.G., Wasserman, W.W., Lenhard, B.: JASPAR: an open access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research 32(1) (2004) (Database Issue)
18. Rahmann, S., Müller, T., Vingron, M.: On the power of profiles for transcription factor binding site detection. Statistical Applications in Genetics and Molecular Biology (Article 7), 2(1) (2003)
19. Roider, H., Kanhere, A., Manke, T., Vingron, M.: Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23(2), 134-141 (2007)