NDLI: Local exact pattern matching for non-fixed RNA structures

Content Provider	ACM Digital Library
Author	Landau, Gad M. Heyne, Steffen Otto, Christina Möhl, Mathias Will, Sebastian Amit, Mika Backofen, Rolf
Copyright Year	2014
Abstract	Detecting local common sequence-structure regions of RNAs is a biologically important problem. Detecting such regions allows biologists to identify functionally relevant similarities 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 on local pattern matching of RNAs, we support the breaking of arcs. This allows us to add flexibility over matching only fixed structures; potentially matching only a similar subset of specified base pairs. We present an $O(n^{3})$ algorithm for local exact pattern matching between two nested RNAs, and an $O(n^{3}$ log $\textit{n})$ algorithm for one nested RNA and one bounded-unlimited RNA. In addition, an algorithm for approximate pattern matching is introduced that for two given nested RNAs and a number $\textit{k},$ finds the maximal local pattern matching score between the two RNAs with at most $\textit{k}$ mismatches in $O(n^{3}k^{2})$ time. Finally, we present an $O(n^{3})$ algorithm for finding the most similar subforest between two nested RNAs.
Starting Page	219
Ending Page	230
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2013.2297113
Volume Number	11
Issue Number	1
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2014-01-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	RNA local similarity Pattern matching Sequence-structure matching Tree local similarity
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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