Large RNA secondary structure conservation annotation using secondary structure-based MSA

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F16%3A10336791" target="_blank" >RIV/00216208:11320/16:10336791 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.17706/ijbbb.2016.6.1.18-25" target="_blank" >http://dx.doi.org/10.17706/ijbbb.2016.6.1.18-25</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.17706/ijbbb.2016.6.1.18-25" target="_blank" >10.17706/ijbbb.2016.6.1.18-25</a>

Result language

angličtina

Original language name

Large RNA secondary structure conservation annotation using secondary structure-based MSA

Original language description

Identification of conserved regions of a set of RNA secondary structures is currently an open research problem when dealing with large RNA molecules such as ribosomal RNA. We designed and implemented a method for conservancy annotation of a set of RNA molecules using their secondary structures. The method first converts secondary structures into linear representations, which are then forwarded into multiple sequence alignment (MSA). The resulting secondary structure-based MSA is subsequently passed into a conservancy identification procedure which uses a sliding window technique to identify conserved position in the MSA and assign them a score based on the secondary structure content of the window. The algorithm can be used to rank overall conservancy of the structures, which generally denotes evolutionary distance, as well as to assign conservancy to individual bases to identify high- or lowconservancy regions. We tested the algorithm for correlation with evolutionary distance, where it matches the expectations. The method is freely available as a stand-alone tool implemented in the Python programming language

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

18-25

UT code for WoS article

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EID of the result in the Scopus database

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