Matching and significance evaluation of combined sequence-structure motifs in RNA

Meyer C, Giegerich R (2002)
ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 216(2/2002): 193-216.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
The discipline of Algebraic Dynamic Programming is a powerful method to design and implement versatile pattern matching algorithms on sequences; here we consider mixed sequence and secondary structure motifs in RNA. A recurring challenge when designing new pattern matchers is to provide a statistical analysis of pattern significance. We demonstrate that by the use of so-called canonical pattern descriptions, the expected number of hits on a sequence of length n can be computed a priori, using the pattern matcher itself. This provides a systematic way to calibrate the specificity of pattern matching algorithms. The technique is exemplified by examples using IRE and SECIS elements.
Erscheinungsjahr
Zeitschriftentitel
ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS
Band
216
Zeitschriftennummer
2/2002
Seite
193-216
ISSN
PUB-ID

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Meyer C, Giegerich R. Matching and significance evaluation of combined sequence-structure motifs in RNA. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS. 2002;216(2/2002):193-216.
Meyer, C., & Giegerich, R. (2002). Matching and significance evaluation of combined sequence-structure motifs in RNA. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS, 216(2/2002), 193-216. doi:10.1524/zpch.2002.216.2.193
Meyer, C., and Giegerich, R. (2002). Matching and significance evaluation of combined sequence-structure motifs in RNA. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 216, 193-216.
Meyer, C., & Giegerich, R., 2002. Matching and significance evaluation of combined sequence-structure motifs in RNA. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS, 216(2/2002), p 193-216.
C. Meyer and R. Giegerich, “Matching and significance evaluation of combined sequence-structure motifs in RNA”, ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS, vol. 216, 2002, pp. 193-216.
Meyer, C., Giegerich, R.: Matching and significance evaluation of combined sequence-structure motifs in RNA. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS. 216, 193-216 (2002).
Meyer, Carsten, and Giegerich, Robert. “Matching and significance evaluation of combined sequence-structure motifs in RNA”. ZEITSCHRIFT FÜR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS 216.2/2002 (2002): 193-216.