title: EvoRSR: an integrated system for exploring evolution of RNA structural robustness.
abstract: BACKGROUND
  Robustness, maintaining a constant phenotype despite perturbations, is a fundamental property of biological systems that is incorporated at various levels of biological complexity. Although robustness has been frequently observed in nature, its evolutionary origin remains unknown. Current hypotheses suggest that robustness originated as a direct consequence of natural selection, as an intrinsic property of adaptations, or as a congruent correlate of environment robustness. To elucidate the evolutionary origins of robustness, a convenient computational package is strongly needed.
  
  
  RESULTS
  In this study, we developed the open-source integrated system EvoRSR (Evolution of RNA Structural Robustness) to explore the evolution of robustness based on biologically important landscapes induced by RNA folding. EvoRSR is object-oriented, modular, and freely available at http://biotech.bmi.ac.cn/EvoRSR under the GNU/GPL license. We present an overview of EvoRSR package and illustrate its features with the miRNA gene cel-mir-357.
  
  
  CONCLUSIONS
  EvoRSR is a novel and flexible package for exploring the evolution of robustness. Accordingly, EvoRSR can be used for future studies to investigate the evolution and origin of robustness and to address other common questions about robustness. While the current EvoRSR environment is a versatile analysis framework, future versions can include features to enhance evolutionary studies of robustness.
authors.affiliation: Beijing Institute of Radiation Medicine, Beijing, PR China. shuwj@bmi.ac.cn
authors.forename: Wenjie
authors.initials: W
authors.lastname: Shu
authors.forename: Ming
authors.initials: M
authors.lastname: Ni
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Zheng
authors.forename: Shengqi
authors.initials: S
authors.lastname: Wang
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology; D019143:Evolution, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*
chemical_list: D012313:RNA
references.citation: J Mol Evol. 2008 Nov;67(5):560-9
references.pmid: 18941828
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W314-9
references.pmid: 17567615
references.citation: Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12306-11
references.pmid: 9770482
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
references.pmid: 12824340
references.citation: PLoS Biol. 2005 Nov;3(11):e381
references.pmid: 16248678
references.citation: Bioinformatics. 2004 Nov 22;20(17):2911-7
references.pmid: 15217813
references.citation: Mol Biol Evol. 2006 Jul;23(7):1427-36
references.pmid: 16679345
references.citation: EMBO Rep. 2006 Feb;7(2):168-73
references.pmid: 16452927
references.citation: Evolution. 1997 Apr;51(2):329-347
references.pmid: 28565347
references.citation: PLoS Comput Biol. 2006 Jan;2(1):e1
references.pmid: 16446784
references.citation: Evolution. 2003 Sep;57(9):1959-72
references.pmid: 14575319
references.citation: Mol Biol Evol. 2006 Nov;23(11):2123-30
references.pmid: 16901984
references.citation: J Exp Zool. 1999 Aug 15;285(2):119-27
references.pmid: 10440723
references.citation: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar;47(3):2083-2099
references.pmid: 9960229
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6593-8
references.pmid: 16608911
references.citation: Eur Biophys J. 1993;22(1):13-24
references.pmid: 7685689
references.citation: Nature. 2000 May 4;405(6782):39-42
references.pmid: 10811210
references.citation: Biopolymers. 1993 Sep;33(9):1389-404
references.pmid: 7691201
references.citation: J Theor Biol. 1998 Oct 21;194(4):491-515
references.pmid: 9790826
references.citation: Proc Biol Sci. 1994 Mar 22;255(1344):279-84
references.pmid: 7517565
references.citation: BMC Evol Biol. 2007 Nov 13;7:223
references.pmid: 17997861