R3D Align
Update - new alignment tools as of 2/2/2024
We are developing new tools to produce nucleotide to nucleotide alignments of RNA chains in PDB structures. They are based on Rfam covariance models, and they work well. Please see the descriptions of the APIs below:
- Text format pairwise alignment or multiple alignment of PDB chains
- Graphical pairwise alignment diagram which represents nucleotide alignments as horizontal bars and represents pairwise interactions within each structure by arcs. An update of the basepair bar diagrams produced by R3D Align.
The R3D Align webserver is no longer running, mostly because we moved to a new server in Fall 2024 and it was too much to get R3D Align running again on the new server. If you want to make alignments between RNA chains that are not in the same Rfam family or clan, you can run R3D Align by downloading it from the GitHub site for R3D Align.
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 alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments.
Availability
The Matlab code behind R3D Align is available at the GitHub site for R3D Align.
Reference
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions. Rahrig et al., Bioinformatics, 2010
Updated: 02/03/2025 05:02PM