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dc.contributor.authorChang, Yen-Fuen_US
dc.contributor.authorHuang, Yen-Linen_US
dc.contributor.authorLu, Chin Lungen_US
dc.date.accessioned2014-12-08T15:11:14Z-
dc.date.available2014-12-08T15:11:14Z-
dc.date.issued2008-07-01en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://dx.doi.org/10.1093/nar/gkn327en_US
dc.identifier.urihttp://hdl.handle.net/11536/8627-
dc.description.abstractSARSA 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/.en_US
dc.language.isoen_USen_US
dc.titleSARSA: a web tool for structural alignment of RNA using a structural alphabeten_US
dc.typeArticleen_US
dc.identifier.doi10.1093/nar/gkn327en_US
dc.identifier.journalNUCLEIC ACIDS RESEARCHen_US
dc.citation.volume36en_US
dc.citation.issueen_US
dc.citation.spageW19en_US
dc.citation.epageW24en_US
dc.contributor.department生物科技學系zh_TW
dc.contributor.department生物資訊及系統生物研究所zh_TW
dc.contributor.departmentDepartment of Biological Science and Technologyen_US
dc.contributor.departmentInstitude of Bioinformatics and Systems Biologyen_US
dc.identifier.wosnumberWOS:000258142300006-
dc.citation.woscount15-
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