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Nucleic Acids Research Advance Access originally published online on May 23, 2008
Nucleic Acids Research 2008 36(Web Server issue):W19-W24; doi:10.1093/nar/gkn327
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W19-W24
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

SARSA: a web tool for structural alignment of RNA using a structural alphabet

Yen-Fu Chang1, Yen-Lin Huang2 and Chin Lung Lu1,3,*

1Institute of Bioinformatics, National Chioa Tung University, 2Department of Computer Science, National Tsing Hua University and 3Department of Biological Science and Technology, National Chioa Tung University, Hsinchu 300, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5712121, ext. 56949; Fax: +886 3 5729288; Email: cllu{at}mail.nctu.edu.tw

Received February 19, 2008. Revised April 30, 2008. Accepted May 7, 2008.

SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. In SARSA, we provide two RNA structural alignment tools, PARTS for pairwise alignment of RNA tertiary structures and MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS, we have implemented four kinds of pairwise alignments for a variety of practical applications: (i) global alignment for comparing whole structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment for finding locally similar substructures and (iv) normalized local alignment for eliminating the mosaic effect of local alignment. Both tools in SARSA take as input RNA 3D structures in the PDB format and in their outputs provide graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA molecules. SARSA is available online at http://bioalgorithm.life.nctu.edu.tw/SARSA/.


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