RNA Secondary Structure Visualization Using Tree Edit Distance

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F16%3A10336792" target="_blank" >RIV/00216208:11320/16:10336792 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.17706/ijbbb.2016.6.1.9-17" target="_blank" >http://dx.doi.org/10.17706/ijbbb.2016.6.1.9-17</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.17706/ijbbb.2016.6.1.9-17" target="_blank" >10.17706/ijbbb.2016.6.1.9-17</a>

Result language

angličtina

Original language name

RNA Secondary Structure Visualization Using Tree Edit Distance

Original language description

RNA secondary structures, both experimental and predicted, are becoming increasingly available which is reflected in the increased demand for tools enabling their analysis. The common first step in the analysis of RNA molecules is visual inspection of their secondary structure. In order to correctly lay out an RNA structure, the notion of optimal layout is required. However, optimal layout of an RNA structure has never been formalized and is largely habitual. To tackle this problem we propose an algorithm capable of visualizing an RNA structure using a related structure with a well-defined layout. The algorithm first converts both structures into tree representations and then uses tree-edit distance algorithm to find out the minimum number of tree edit operations to convert one structure into the other. We couple each tree edit operation with a layout modification operation which is then used to gradually transform the known layout into the target one. The tree edit distance algorithm causes that the common motives are retained and only regions which differ in both the structures are changed in the resulting layout. Visual inspection and planarity evaluation reveals that the algorithm is able to give good layouts even for relatively distant structures while keeping the layout planar. The new method is well suited for situations when one needs to visualize a structure for which a homologous structure with a good visualization is already available.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

IN - Informatics

OECD FORD branch

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Project

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Continuities

S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

International Journal of Bioscience, Biochemistry and Bioinformatics

ISSN

2010-3638

e-ISSN

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Volume of the periodical

6

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

8

Pages from-to

9-17

UT code for WoS article

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EID of the result in the Scopus database

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