Title: iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
Authors: Wang, Chih-Wei
Chen, Kun-Tze
Lu, Chin Lung
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
Issue Date: 1-Jul-2010
Abstract: iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudotorsion angles g and h. Next, we apply the affinity propagation clustering algorithm to this g-h plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/.
URI: http://dx.doi.org/10.1093/nar/gkq483
ISSN: 0305-1048
DOI: 10.1093/nar/gkq483
Volume: 38
Begin Page: W340
End Page: W347
Appears in Collections:Articles

Files in This Item:

  1. 000284148900054.pdf