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/.

Figure 1.

The web interface of iPARTS2.

Figure 2.

ROC curves for d = 0 based on the SAS values of all aligned pairs of RNA 3D structures in the FSCOR dataset, where the AUC values of iPARTS, SARA, SETTER and iPARTS2 are 0.861, 0.883, 0.843 and 0.914, respectively. Note that the AUC value of RASS computed by using the 67006 pairs of RNA 3D structures is 0.892.

Figure 3.

ROC curves for d ≤ 2 based on the SAS values of all aligned pairs of RNA 3D structures in the FSCOR dataset, where the AUC values of iPARTS, SARA, SETTER and iPARTS2 are 0.740, 0.761, 0.713 and 0.772, respectively. Note that the AUC value of RASS computed by using the 67006 pairs of RNA 3D structures is 0.758.