FledFold: A Novel Software for RNA Secondary Structure Prediction

Background: RNA secondary structure is essential to understand the mechanism of RNAs. Method: In this paper, fledFold, a novel software for RNA secondary structure prediction, is introduced. It combines both thermodynamic and kinetic factors of RNA secondary structures and can predict RNA secondary structures from their primary sequences with local personal computers. Results: FledFold is implemented in C++ under Windows 7 and could run on windows 7 or later version with at least 2 GB of RAM. Fledfold is user friendly and could output results with multiple formats. Conslusion: FledFold will be a valuable tool for RNA researches and it could be downloaded freely from http://www.jlucomputer.com/fledfold.php

[1]  J. Mattick,et al.  Non-coding RNA. , 2006, Human molecular genetics.

[2]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[3]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[4]  H. Schwalbe,et al.  NMR Spectroscopy of RNA , 2003, Chembiochem : a European journal of chemical biology.

[5]  Yang Li,et al.  A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation , 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[6]  David H. Mathews,et al.  NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure , 2009, Nucleic Acids Res..

[7]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[8]  D. Mathews,et al.  Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.

[9]  Ligang Wu,et al.  Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs. , 2008, Molecular cell.

[10]  J. Mattick.  The Functional Genomics of Noncoding RNA , 2005, Science.

[11]  D. Mathews,et al.  ProbKnot: fast prediction of RNA secondary structure including pseudoknots. , 2010, RNA.

[12]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

[13]  G. Mauri,et al.  An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences , 2008, Journal of Computer Science and Technology.

[14]  John S Mattick,et al.  Probing the phenomics of noncoding RNA , 2013, eLife.

[15]  Carl R. Woese,et al.  4 Probing RNA Structure, Function, and History by Comparative Analysis , 1993 .

[16]  M. Spencer.  X-ray Diffraction Studies of the Secondary Structure of RNA , 1963 .

[17]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Wolfgang Wintermeyer,et al.  How ribosomes make peptide bonds. , 2007, Trends in biochemical sciences.

[19]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[20]  H. Schwalbe,et al.  NMR Spectroscopy of RNA , 2003, Chembiochem : a European journal of chemical biology.