title: ERD: a fast and reliable tool for RNA design including constraints.
abstract: BACKGROUND
  The function of an RNA in cellular processes is directly related to its structure. The free energy of RNA structure in another important key to its function as only some structures with a specific level of free energy can take part in cellular reactions. Therefore, to perform a specific function, a particular RNA structure with specific level of free energy is required. For a given RNA structure, the goal of the RNA design problem is to design an RNA sequence that folds into the given structure. To mimic the biological features of RNA sequences and structures, some sequence and energy constraints should be considered in designing RNA. Although the level of free energy is important, it is not considered in the available approaches for RNA design problem.
  
  
  RESULTS
  In this paper, we present a new version of our evolutionary algorithm for RNA design problem, entitled ERD, and extend it to handle some sequence and energy constraints. In the sequence constraints, one can restrict sequence positions to a fixed nucleotide or to a subset of nucleotides. As for the energy constraint, one can specify an interval for the free energy ranges of the designed sequences. We compare our algorithm with INFO-RNA, MODENA, NUPACK, and RNAiFold approaches for some artificial and natural RNA secondary structures and constraints.
  
  
  CONCLUSIONS
  The results indicate that our algorithm outperforms the other mentioned approaches in terms of accuracy, speedup, divergency, nucleotides distribution, and similarity to the natural RNA sequences. Particularly, the designed RNA sequences in our method are much more reliable and similar to the natural counterparts. The generated sequences are more diverse and they have closer nucleotides distribution to the natural one. The ERD tool and web server are freely available at http://mostafa.ut.ac.ir/corna/erd-cons/ .
authors: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. aliesmaili@ut.ac.ir.
authors: Ali
authors: A
authors: Esmaili-Taheri
authors: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, College of Science, University of Tehran, Tehran, Iran. mgtabesh@ut.ac.ir.|Laboratoire d'Informatique (LIX), Ecole Polytechnique, Palaiseau CEDEX, 91128, France. mgtabesh@ut.ac.ir.
authors: Mohammad
authors: M
authors: Ganjtabesh
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA
references: Bioinformatics. 2006 Aug 1;22(15):1823-31
references: 16709587
references: Bull Math Biol. 1999 May;61(3):437-67
references: 17883226
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: Front Genet. 2012 Apr 26;3:36
references: 22558001
references: Bioinformatics. 2014 May 1;30(9):1250-8
references: 24407223
references: BMC Bioinformatics. 2011 Aug 03;12:319
references: 21813013
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W310-3
references: 17452349
references: J Mol Biol. 2004 Feb 20;336(3):607-24
references: 15095976
references: Plant Cell. 2006 May;18(5):1121-33
references: 16531494
references: J Bioinform Comput Biol. 2013 Apr;11(2):1350001
references: 23600819
references: Nature. 2004 Mar 18;428(6980):263-4
references: 15029175
references: Algorithms Mol Biol. 2009 Feb 09;4:4
references: 19203377
references: J Comput Chem. 2011 Feb;32(3):439-52
references: 20717905
references: J Mol Biol. 1999 May 21;288(5):911-40
references: 10329189
references: J Mol Biol. 1970 Mar;48(3):443-53
references: 5420325
references: BMC Bioinformatics. 2012 Oct 09;13:260
references: 23043260
references: Adv Appl Bioinform Chem. 2011;4:1-12
references: 21918633
references: Biotechniques. 2001 Dec;31(6):1320-4
references: 11768661
references: BMC Bioinformatics. 2007 Jan 31;8:34
references: 17266771
references: J Biomol Struct Dyn. 2008 Aug;26(1):147-62
references: 18533734
references: Bioinformatics. 2009 Aug 1;25(15):1974-5
references: 19398448
references: Bioinformatics. 2013 Jul 01;29(13):i308-15
references: 23812999
references: Biopolymers. 2013 Dec;99(12):1124-36
references: 23818234