TRAVeLer: a tool for template-based RNA secondary structure visualization
Jazyk angličtina Země Velká Británie, Anglie Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
15-00885S
Grantová Agentura České Republiky (CZ)
PubMed
29141608
PubMed Central
PMC5688744
DOI
10.1186/s12859-017-1885-4
PII: 10.1186/s12859-017-1885-4
Knihovny.cz E-zdroje
- Klíčová slova
- RNA secondary structure, Software tool, Template-based modeling, Visualization,
- MeSH
- algoritmy MeSH
- konformace nukleové kyseliny MeSH
- RNA chemie MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- RNA MeSH
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 .
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