title: RNAMST: efficient and flexible approach for identifying RNA structural homologs.
abstract: RNA molecules fold into characteristic secondary structures for their diverse functional activities such as post-translational regulation of gene expression. Searching homologs of a pre-defined RNA structural motif, which may be a known functional element or a putative RNA structural motif, can provide useful information for deciphering RNA regulatory mechanisms. Since searching for the RNA structural homologs among the numerous RNA sequences is extremely time-consuming, this work develops a data preprocessing strategy to enhance the search efficiency and presents RNAMST, which is an efficient and flexible web server for rapidly identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences. Intuitive user interface are provided on the web server to facilitate the predictive analysis. By comparing the proposed web server to other tools developed previously, RNAMST performs remarkably more efficiently and provides more effective and flexible functions. RNAMST is now available on the web at http://bioinfo.csie.ncu.edu.tw/~rnamst/.
authors.affiliation: Department of Computer Science and Information Engineering, National Central University, Chung-Li 320, Taiwan.
authors.forename: Tzu-Hao
authors.initials: TH
authors.lastname: Chang
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.forename: Tzu-Neng
authors.initials: TN
authors.lastname: Chuang
authors.forename: Dray-Ming
authors.initials: DM
authors.lastname: Shien
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
mesh_terms: D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D012313:RNA