title: iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.
abstract: Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30050, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan.
authors.forename: Chung-Han
authors.initials: CH
authors.lastname: Yang
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Cheng-Ting
authors.initials: CT
authors.lastname: Shih
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Kun-Tze
authors.initials: KT
authors.lastname: Chen
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Po-Han
authors.initials: PH
authors.lastname: Lee
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Ping-Han
authors.initials: PH
authors.lastname: Tsai
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Jian-Cheng
authors.initials: JC
authors.lastname: Lin
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
authors.forename: Ching-Yu
authors.initials: CY
authors.lastname: Yen
authors.affiliation: Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30050, Taiwan.
authors.forename: Tiao-Yin
authors.initials: TY
authors.lastname: Lin
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan cllu@cs.nthu.edu.tw.
authors.forename: Chin Lung
authors.initials: CL
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D003196:Computer Graphics; D020407:Internet; D015233:Models, Statistical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011387:Prokaryotic Cells / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D014584:User-Computer Interface
chemical_list: D012313:RNA