An Overview of
            RNA
            Structure Prediction and Applications to
            RNA
            Gene Prediction and
            RNA
            i Design

AbstractTo compare the secondary structures of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure at single-nucleotide resolution using sequence information, and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modelling. CROSSalign can be applied to perform pair-wise comparisons and is able to find homologues between thousands of matches identifying the exact regions of similarity between profiles of different lengths. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/CROSSalign.

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Algorithm and Scheme in RNA Structure Prediction Including Pseudoknots

2018 14th International Conference on Computational Intelligence and Security (CIS) ◽

10.1109/cis2018.2018.00050 ◽

2018 ◽

Author(s):

Zhendong Liu ◽

Fanghan Liu ◽

Qingxia Kong ◽

Fanchang Hao ◽

Hongluan Zhao

Keyword(s):

Rna Structure ◽

Structure Prediction ◽

Rna Structure Prediction

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reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction

BMC Bioinformatics ◽

10.1186/s12859-019-2645-4 ◽

2019 ◽

Vol 20 (S3) ◽

Cited By ~ 1

Author(s):

Risa Kawaguchi ◽

Hisanori Kiryu ◽

Junichi Iwakiri ◽

Jun Sese

Keyword(s):

High Throughput ◽

Rna Structure ◽

Structure Prediction ◽

Rna Structure Prediction

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Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.325-326.1551 ◽

2013 ◽

Vol 325-326 ◽

pp. 1551-1554

Author(s):

Yi Qi

Keyword(s):

Secondary Structure ◽

Sensitivity And Specificity ◽

Rna Structure ◽

Structure Prediction ◽

Rna Secondary Structure ◽

Experimental Results ◽

New Method ◽

Rna Structure Prediction ◽

New Strategies

In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.

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