Paper Info
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/.
Year
DOI
Venue
2016
10.1093/nar/gkw412
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Sequence alignment,RNA,Pairwise comparison,Structural alignment,Biology,Algorithm,Bioinformatics,Genetics,Computer graphics,Base pair,Web server,Alphabet
Journal
44
Issue
ISSN
Citations 
W1
0305-1048
0
PageRank 
References 
Authors
0.34
7
9
Name
Order
Citations
PageRank
chunghan yang1212.21
Cheng-Ting Shih200.34
Kun-Tze Chen3504.63
Po-Han Lee400.34
Ping-Han Tsai500.34
Jian-Cheng Lin6243.39
Ching-Yu Yen700.68
Tiao-Yin Lin800.34
Chin Lung Lu942334.59