Abstract
BackgroundUnderstanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm.ResultsIn this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated.ConclusionTo the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
Highlights
Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures
While in a pairwise structure alignment biological relationships are inferred from structure similarity, with a multiple alignment we already know that structures are biologically related and we are looking for key features preserved by evolution that are difficult to identify by a pairwise alignment
SETTER algorithm In the SETTER (SEcondary sTructure-based TERtiary superposition) algorithm, RNA structures are divided into secondary-structure based fragments called generalized secondary structure units (GSSU) [21]
Summary
Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. Though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Several methods and servers for pairwise RNA structure comparison and alignment exist, including ARTS [8, 9], DIAL [10], iPARTS [11], SARA [12, 13], SARSA [14], Rclick [15, 16], R3Dalign [17, 18], RASS [19], FRASS [20], SETTER [21, 22] or R3D-BLAST [23]. While in a pairwise structure alignment biological relationships are inferred from structure similarity, with a multiple alignment we already know that structures are biologically related and we are looking for key features preserved by evolution that are difficult to identify by a pairwise alignment
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