scholarly journals BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Julien Allali ◽  
Cédric Saule ◽  
Cédric Chauve ◽  
Yves d’Aubenton-Carafa ◽  
Alain Denise ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Fundamental Problem ◽  
Pairwise Comparison ◽  
Secondary Structures ◽  
Software Tools ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Ordered Trees ◽  
Synthetic Datasets ◽  
Comparison Algorithms

The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets.

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.

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

scholarly journals Graphical Processing Unit - Supported RNA Secondary Structure Comparison

10.29007/bhsr ◽  
2020 ◽  
Author(s):  
Mutlu Mete ◽  
Abdullah Arslan
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Secondary Structures ◽  
Graphical Processing Unit ◽  
Processing Unit ◽  
Structure Comparison ◽  
Rna Secondary Structures ◽  
Large Databases ◽  
Graphical Processing ◽  
Rna Secondary Structure Comparison

This study is part of our perpetual effort to develop improved RNA secondary structure analysis tools and databases. In this work we present a new Graphical Processing Unit (GPU)-based RNA structural analysis framework that supports fast multiple RNA secondary structure comparison for very large databases. A search-based secondary structure comparison algorithm deployed in RNASSAC website helps bioinformaticians find common RNA substructures from the underlying database. The algorithm performs two levels of binary searches on the database. Its time requirement is affected by the database size. Experiments on the RNASSAC website show that the algorithm takes seconds for a database of 4,666 RNAs. For example, it takes about 4.4 sec for comparing 25 RNAs from this database. In another case, when many non-overlapping common substructures are desired, a heuristic approach requires as long as 85 sec in comparing 40 RNAs from the same database. The comparisons by this sequential algorithm takes at least 50% more time when RNAs are compared from the database of several millions of RNAs. The most recently curated databases already have millions of RNA secondary structures. The improvement in run-time performance of comparison algorithms is necessary. This study present a GPU-based RNA substructure comparison algorithm with which running time for multiple RNA secondary structures remains feasible for large databases. Our new parallel algorithm is 12 times faster than the CPU version (sequential) comparison algorithm of the RNASSAC website. The response time significantly reduces towards development of a realtime RNA comparison web service for bioinformatics community.

scholarly journals Graph-Based Analysis of RNA Secondary Structure Similarity Comparison

Complexity ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Lina Yang ◽  
Yang Liu ◽  
Xiaochun Hu ◽  
Patrick Wang ◽  
Xichun Li ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Noncoding Rna ◽  
Graphical Representation ◽  
Rna Virus ◽  
Distance Matrix ◽  
Secondary Structures ◽  
Discrete Wavelet ◽  
Rna Secondary Structures ◽  
Clustering Tree

In organisms, ribonucleic acid (RNA) plays an essential role. Its function is being discovered more and more. Due to the conserved nature of RNA sequences, its function mainly depends on the RNA secondary structure. The discovery of an approximate relationship between two RNA secondary structures helps to understand their functional relationship better. It is an important and urgent task to explore structural similarities from the graphical representation of RNA secondary structures. In this paper, a novel graphical analysis method based on the triple vector curve representation of RNA secondary structures is proposed. A combinational method involving a discrete wavelet transform (DWT) and fractal dimension with sliding window is introduced to analyze and compare the graphs derived from feature extraction; after that, the distance matrix is generated. Then, the distance matrix is analyzed by clustering and visualized as a clustering tree. RNA virus and noncoding RNA datasets are applied to perform experiments and analyze the clustering tree. The results show that the proposed method yields more accurate results in the comparison of RNA secondary structures.

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
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