RNA: Structure, Prediction, and Visualization Tools

RNA has been found to be associated with many diseases, especially in humans. To understand the correlation of RNA with disease, an individual needs to understand its structure. As prediction of three-dimensional structure of RNA is complex and costly affair, researchers are focusing on the secondary structure of RNA. RNA secondary structure has been predicted by various algorithms, and various tools have been developed for its automatic prediction. Several components of RNA secondary structure have been acknowledged, namely hairpin loop, stacked pair, bulge loop, internal loop, and junction. The motive of this paper is to explore various RNA structures, techniques prediction of RNA secondary structure, and visualizations tools.

[1]  E Rivas,et al.  A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.

[2]  Bjarne Knudsen,et al.  RNA secondary structure prediction using stochastic context-free grammars and evolutionary history , 1999, Bioinform..

[3]  S. Ying,et al.  Intronic MicroRNA (miRNA) , 2006, Journal of biomedicine & biotechnology.

[4]  Kay C. Wiese,et al.  Permutation-based RNA secondary structure prediction via a genetic algorithm , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[5]  Jie Quan,et al.  QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization , 2015, BMC Genomics.

[6]  Sankar K. Pal,et al.  RNA Secondary Structure Prediction Using Soft Computing , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  Anne Condon,et al.  Problems on RNA Secondary Structure Prediction and Design , 2003, ICALP.

[8]  Weixiong Zhang,et al.  An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots , 2004, Bioinform..

[9]  Olga Golosova,et al.  Unipro UGENE: a unified bioinformatics toolkit , 2012, Bioinform..

[10]  Dolly Sharma,et al.  RNA Secondary Structure Prediction Algorithms Including Pseudoknots , 2013 .

[11]  S. Salzberg,et al.  Fast algorithms for large-scale genome alignment and comparison. , 2002, Nucleic acids research.

[12]  Elena Rivas,et al.  The language of RNA: a formal grammar that includes pseudoknots , 2000, Bioinform..

[13]  Aleksey Y. Ogurtsov,et al.  A periodic pattern of mRNA secondary structure created by the genetic code , 2006, Nucleic acids research.

[14]  D. Hillis,et al.  Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. , 1993, Molecular biology and evolution.

[15]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[16]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[17]  Tatsuya Akutsu,et al.  Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots , 2000, Discret. Appl. Math..

[18]  Jacques Cohen,et al.  Bioinformatics—an introduction for computer scientists , 2004, CSUR.

[19]  S. Brenner,et al.  RNA structural motifs: building blocks of a modular biomolecule , 2005, Quarterly Reviews of Biophysics.

[20]  Anne Condon,et al.  RNAsoft: a suite of RNA secondary structure prediction and design software tools , 2003, Nucleic Acids Res..

[21]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[22]  Allen R. Buskirk,et al.  Genetic Analysis of the Structure and Function of Transfer Messenger RNA Pseudoknot 1* , 2006, Journal of Biological Chemistry.

[23]  A. Rich,et al.  Transfer RNA: molecular structure, sequence, and properties. , 1976, Annual review of biochemistry.

[24]  S. Eddy.  Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.

[25]  Andreas Prlic,et al.  Sequence analysis , 2003 .

[26]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[27]  Christian Zwieb,et al.  A nomenclature for all signal recognition particle RNAs. , 2005, RNA.