RNA Pseudoknot Prediction Using Term Rewriting

Fu, Xuezheng; Wang, H.; Harrison, William L.; Harrison, Robert W.

doi:10.1109/bibe.2005.50

Cited by 4 publications

(3 citation statements)

References 19 publications

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“…Additionally, a non-mixing insertion/deletion system that models part of the RNA-editing for kinetoplastids is given. A rather different application of term rewriting in the setting of RNA is reported in [4], where the rewrite engine of Maude is exploited to predict the occurrence of specific patterns in the spatial formation of RNA, with competitive precision compared to techniques that are more frequently used in bioinformatics.…”

Section: Related Work and Concluding Remarksmentioning

confidence: 99%

Combining Insertion and Deletion in RNA-editing Preserves Regularity

Vink

Zantema

Bošnački

2012

Electron. Proc. Theor. Comput. Sci.

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Inspired by RNA-editing as occurs in transcriptional processes in the living cell, we introduce an abstract notion of string adjustment, called guided rewriting. This formalism allows simultaneously inserting and deleting elements. We prove that guided rewriting preserves regularity: for every regular language its closure under guided rewriting is regular too. This contrasts an earlier abstraction of RNA-editing separating insertion and deletion for which it was proved that regularity is not preserved. The particular automaton construction here relies on an auxiliary notion of slice sequence which enables to sweep from left to right through a completed rewrite sequence.

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Section: Related Work and Concluding Remarksmentioning

confidence: 99%

Combining Insertion and Deletion in RNA-editing Preserves Regularity

Vink

Zantema

Bošnački

2012

Electron. Proc. Theor. Comput. Sci.

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“…Pseudoknots can be defined as follows: If R is an RNA sequence such that R = r 1 , r 2 , r 3 , r 4 ...r n , and (r x r y ) and (r p r q ) are two different base pairs existing in this RNA structure (x < y and p < q), a pseudoknot is composed of these two base pairs when 1 ≤ x < p < y < q ≤ n [13]. Simply stated, a Pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which a section of one stem is intercalated between the two sections of another stem.…”

Section: Rna Secondary Structuresmentioning

confidence: 99%

A Matrix Algorithm for RNA Secondary Structure Prediction

Krishnan

Khurshid

Veeravalli

2010

Pattern Recognition in Bioinformatics

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In this paper we propose a novel high-performance algorithm, referred to as MARSs (Matrix Algorithm for RNA Secondary Structure Prediction), for predicting RNA Secondary Structures with or without pseudoknots. The algorithm is capable of operating in both serial and parallel modes. The algorithm will take complete advantage of the explicit hardware parallelism increasingly available in todayś multi-core processors resulting in execution speedups. Unlike Dynamic Programming based algorithms, MARSs is non-recursive by design and therefore eliminates some of the disadvantages of Dynamic Programming based algorithms. We performed a large-scale experiment on a multi-core hardware using real sequences with verified structures. We detail and discuss the results from these experiments using metrics such as performance gains, run-times and prediction accuracy. This is one of the first attempts of its kind to provide a complete flexibility in evolving a RNA secondary structure with or without pseudoknots using a matrix-based approach.

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“…Additionally, a non-mixing insertion/deletion system that models part of the RNA-editing for kinetoplastids is given. A rather different application of term rewriting in the setting of RNA is reported in [8], where the rewrite engine of Maude is exploited to predict the occurrence of specific patterns in the spatial formation of RNA, with competitive precision compared to techniques that are more frequently used in bioinformatics.…”

Section: Related Work and Concluding Remarksmentioning

confidence: 99%

RNA-Editing with Combined Insertion and Deletion Preserves Regularity

Vink¹,

Zantema²,

Bošnački³

2013

SACS

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We consider two elementary forms of string rewriting called guided insertion/deletion and guided rewriting. The original strings are modified depending on the match with a given set of auxiliary strings, called guides. Guided insertion/deletion considers matching of a string and a guide with respect to a specific correspondence of strings. Guided rewriting considers matching of a string and a guide with respect to an equivalence relation on the alphabet. Guided insertion/deletion is inspired by RNA-editing, a biological process by which the original genetic information stored in DNA is modified before its final expression. The formalism here allows for simultaneous insertion and deletion of string elements. Guided rewriting, based on a letter-to-letter relation, is technically more appealing than guided insertion/deletion. We prove that guided rewriting preserves regularity: for every regular language its closure under guided rewriting is regular too. In the proof we will rely on the auxiliary notion of a slice sequence. We establish a correspondence of slice sequences and guide rewrite sequences. Because of their left-to-right nature, slice sequences are more convenient to deal with than guided rewrite sequences in the construction of the finite automata that we encounter in the proofs of regularity. Based on the result for guided rewriting we establish that guided insertion/deletion preserves regularity as well.

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RNA Pseudoknot Prediction Using Term Rewriting

Cited by 4 publications

References 19 publications

Combining Insertion and Deletion in RNA-editing Preserves Regularity

Combining Insertion and Deletion in RNA-editing Preserves Regularity

A Matrix Algorithm for RNA Secondary Structure Prediction

RNA-Editing with Combined Insertion and Deletion Preserves Regularity

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