Title: R3D-BLAST: a search tool for similar RNA 3D substructures
Authors: Liu, Yun-Chen
Yang, Chung-Han
Chen, Kun-Tze
Wang, Jyun-Rong
Cheng, Mei-Ling
Chung, Jen-Chun
Chiu, Hsien-Tai
Lu, Chin Lung
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
Issue Date: 1-Jul-2011
Abstract: R3D-BLAST is a BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea behind R3D-BLAST is that all the RNA 3D structures deposited in the PDB are first encoded as 1D structural sequences using a structural alphabet of 23 distinct nucleotide conformations, and BLAST is then applied to these 1D structural sequences to search for those RNA substructures whose 1D structural sequences are similar to that of the query RNA substructure. R3D-BLAST takes as input an RNA 3D structure in the PDB format and outputs all substructures of the hits similar to that of the query with a graphical display to show their structural superposition. In addition, each RNA substructure hit found by R3D-BLAST has an associated E-value to measure its statistical significance. R3D-BLAST is now available online at http://genome.cs.nthu.edu.tw/R3D-BLAST/ for public access.
URI: http://dx.doi.org/10.1093/nar/gkr379
ISSN: 0305-1048
DOI: 10.1093/nar/gkr379
Volume: 39
Begin Page: W45
End Page: W49
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