Local Exact Pattern Matching for Non-fixed RNA Structures

机译：非固定RNA结构的局部精确模式匹配

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Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n~3) algorithm for local exact pattern matching between two nested RNAs, and an O(n~3 log n) algorithm for one nested RNA and one bounded-unlimited RNA.

机译：检测RNA的局部共有序列结构区域是生物学上有意义的问题。通过检测这样的区域，生物学家能够识别被检查分子之间的功能相似性。我们开发了动态编程算法来查找两个RNA之间的常见结构序列模式。 RNA由其序列和一组具有相关概率的潜在碱基对给出。与匹配固定结构的现有工作相比，我们支持弧断编辑操作。这仅允许匹配给定碱基对的一个子集。我们提出了O（n〜3）算法用于两个嵌套RNA之间的局部精确模式匹配，以及O（n〜3 log n）算法用于一个嵌套RNA和一个有界无限的RNA。

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《Combinatorial pattern matching》|2012年|306-320|共15页
会议地点 Helsinki(FI)
作者
Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Moehl; Christina Schmiedl; Sebastian Will;
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Department of Computer Science, University of Haifa, Mount Carmel, Haifa, Israel;

Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany,Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-Universitat, Freiburg, Germany;

Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany;

Department of Computer Science, University of Haifa, Mount Carmel, Haifa, Israel,Department of Computer Science and Engineering, NYU-Poly, Brooklyn NY, USA;

Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany;

Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany;

Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universitat, Freiburg, Germany,CSAIL and Mathematics Department, MIT, Cambridge MA, USA;

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专利

1. Local Exact Pattern Matching for Non-FixedRNA Structures [J] . Amit M., Backofen R., Heyne S., Computational Biology and Bioinformatics, IEEE/ACM Transactions on . 2014,第1期

机译：非固定RNA结构的局部精确模式匹配
2. Exact matching of RNA secondary structure patterns [J] . Xu Y, Wang LS, Zhao H, Theoretical computer science . 2005,第1期

机译：RNA二级结构模式的精确匹配
3. ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs [J] . Christina Otto, Mathias M?hl, Steffen Heyne, BMC Bioinformatics . 2014,第1期

机译：Exparna-P：同时同时进行精确的模式匹配和折叠RNA
4. Local Exact Pattern Matching for Non-fixed RNA Structures [C] . Mika Amit, Rolf Backofen, Steffen Heyne, Annual Symposium on Combinatorial Pattern Matching . 2012

机译：用于非固定RNA结构的局部精确模式
5. Pattern Matching Statistics in the Permtutations Sn and the Alternating Permutations An for Minimally Overlapping Patterns [D] . Duane, Adrian Scott 2013

机译：最小重叠图案中置换Sn和交替置换An中的模式匹配统计量
6. ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs [O] . Christina Otto, Mathias Möhl, Steffen Heyne, 2014

机译：ExpaRNA-P：RNA的同时精确模式匹配和折叠
7. Local Exact Pattern Matching for Non-Fixed RNA Structures [O] . Mika Amit, Rolf Backofen, Steffen Heyne, 2015

机译：非固定RNa结构的局部精确模式匹配
8. Primary Child Care Arrangements of U.S. Infants: Patterns of Utilization by Poverty Status, Family Structure, Maternal Work Status, Family Structure, Maternal Work Status, Maternal Work Schedule, and Child Care Assistance. Research Brief [R] . Halle, T., Hair, E., Nuenning, M., 2009

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Local Exact Pattern Matching for Non-fixed RNA Structures

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