BACKGROUND: Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. RESULTS: This article introduces Traveler, a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. CONCLUSIONS: Traveler is a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout. It is available at http://github.com/davidhoksza/traveler .

Faculty of Mathematics and Physics Charles University Prague 11800 Czech Republic

Zobrazit více v PubMed

Wiese KC, Glen E, Vasudevan A. jViz.Rna - A java tool for RNA secondary structure visualization. IEEE Trans Nanobioscience. 2005;4(3):212–8. doi: 10.1109/TNB.2005.853646. PubMed DOI

Auber D, Delest M, Domenger JP, Dulucq S. Efficient drawing of RNA secondary structure. J Graph Algorithms Appl. 2006;10(2):329–51. doi: 10.7155/jgaa.00131. DOI

Ponty Y, Leclerc F. Drawing and editing the secondary structure(s) of RNA. In: RNA Bioinforma. Springer: 2015. p. 63–100. PubMed

Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009;25(15):1974–1975. doi: 10.1093/bioinformatics/btp250. PubMed DOI PMC

Lorenz R, Bernhart SH, zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. {ViennaRNA} Package 2.0. Algorithms Mol Biol. 2011;6(1):26. doi: 10.1186/1748-7188-6-26. PubMed DOI PMC

Hecker N, Wiegels T, Torda AE. RNA secondary structure diagrams for very large molecules: RNAfdl. Bioinformatics. 2013;29(22):2941–942. doi: 10.1093/bioinformatics/btt496. PubMed DOI

Elias R, Hoksza D. Rna secondary structure visualization using tree edit distance. Int J Biosci Biochem Bioinforma. 2016;6(1):9.

De Rijk P, De Wachter R. RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res. 1997;25(22):4679–684. doi: 10.1093/nar/25.22.4679. PubMed DOI PMC

De Rijk P, Wuyts J, De Wachter R. Rna Viz 2: An improved representation of RNA secondary structure. Bioinforma. 2003;19(2):299–300. doi: 10.1093/bioinformatics/19.2.299. PubMed DOI

Tai KC. The Tree-to-Tree Correction Problem. J ACM. 1979;26(3):422–33. doi: 10.1145/322139.322143. DOI

Zhang K, Shasha D. Simple Fast Algorithms for the Editing Distance between Trees and Related Problems. SIAM J Comput. 1989;18(6):1245–1262. doi: 10.1137/0218082. DOI

Demaine ED, Mozes S, Rossman B, Weimann O. An optimal decomposition algorithm for tree edit distance. ACM Trans Algorithms. 2009;6(1):1–19. doi: 10.1145/1644015.1644017. DOI

Pawlik M, Augsten N. RTED : A Robust Algorithm for the Tree Edit Distance. In: The 38th Int Conf on Very Large Data Bases.2011. p. 334–345.

Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2. doi: 10.1186/1471-2105-3-2. PubMed DOI PMC

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P. An update on lncipedia: a database for annotated human lncrna sequences. Nucleic Acids Res. 2014;43(D1):174–80. doi: 10.1093/nar/gku1060. PubMed DOI PMC

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