title: taveRNA: a web suite for RNA algorithms and applications.
abstract: We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic programming solution that minimizes the sum of energy density and free energy of an RNA structure. inteRNA is the first RNA-RNA interaction structure prediction web service. It also employs a dynamic programming algorithm to minimize the free energy of the resulting joint structure of the two interacting RNAs. Lastly, pRuNA is an efficient database pruning service; which given a query RNA, eliminates a significant portion of an ncRNA database and returns only a few ncRNAs as potential regulators. taveRNA is available at http://compbio.cs.sfu.ca/taverna.
authors.affiliation: Lab for Computational Biology, SFU, Canada.
authors.forename: Cagri
authors.initials: C
authors.lastname: Aksay
authors.forename: Raheleh
authors.initials: R
authors.lastname: Salari
authors.forename: Emre
authors.initials: E
authors.lastname: Karakoc
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Sahinalp
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D020407:Internet; D008956:Models, Chemical; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011381:Programming Languages; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA