An efficient seeded tree alignment algorithm for finding the similarity score of two RNA secondary structures

2010 ◽  
Author(s):  
Mohammad Shamsur Rahman ◽  
Abul Kashem Mia
Keyword(s):  
Secondary Structures ◽  
Similarity Score ◽  
Alignment Algorithm ◽  
Rna Secondary Structures ◽  
Tree Alignment

scholarly journals An algebraic representation for tree alignment of RNA pseudoknotted structures

2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  
Keyword(s):  
Secondary Structures ◽  
Algebraic Representation ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Tree Alignment ◽  
Ordered Trees ◽  
Multiple Context ◽  
Alignment Problem ◽  
Definition Of ◽  
Context Free

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.

scholarly journals An algebraic representation for tree alignment of RNA pseudoknotted structures

2017 ◽  
Author(s):  
Michela Quadrini ◽  
Luca Tesei ◽  
Emanuela Merelli ◽  
Keyword(s):  
Secondary Structures ◽  
Algebraic Representation ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Tree Alignment ◽  
Ordered Trees ◽  
Multiple Context ◽  
Alignment Problem ◽  
Definition Of ◽  
Context Free

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.

scholarly journals Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli

RNA ◽  
2016 ◽  
Vol 22 (11) ◽  
pp. 1739-1749 ◽  
Author(s):  
Knut I. Kristiansen ◽  
Ragnhild Weel-Sneve ◽  
James A. Booth ◽  
Magnar Bjørås
Keyword(s):  
Escherichia Coli ◽  
Translation Initiation ◽  
Secondary Structures ◽  
Rna Secondary Structures

Interval-Based Similarity for Classifying Conserved RNA Secondary Structures

2016 ◽  
Vol 31 (3) ◽  
pp. 78-85 ◽  
Author(s):  
Qingfeng Chen ◽  
Yi-Ping Phoebe Chen ◽  
Chengqi Zhang
Keyword(s):  
Secondary Structures ◽  
Rna Secondary Structures

scholarly journals Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20561 ◽  
Author(s):  
Paul M. Krzyzanowski ◽  
Feodor D. Price ◽  
Enrique M. Muro ◽  
Michael A. Rudnicki ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Expressed Sequence Tag ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rna ◽  
Expressed Sequence

scholarly journals Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

Biochimie ◽  
2011 ◽  
Vol 93 (11) ◽  
pp. 2019-2023 ◽  
Author(s):  
Sven Findeiß ◽  
Jan Engelhardt ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Secondary Structures ◽  
Protein Coding ◽  
Rna Secondary Structures ◽  
Coding Regions

Large-scale Investigation of Long Noncoding RNA Secondary Structures in Human and Mouse

2018 ◽  
Vol 13 (5) ◽  
pp. 450-460 ◽  
Author(s):  
Xingli Guo ◽  
Lin Gao ◽  
Yu Wang ◽  
David K.Y. Chiu ◽  
Bingbo Wang ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Large Scale ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Human And Mouse
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