R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.

ABSTRACT:

Motivation

Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the 'local alignment' graph.

Results

The algorithm is implemented in a program suite and web server called 'R3D Align'. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand al

SUBMITTER: Rahrig RR 

PROVIDER: S-EPMC3465099 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature