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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

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

Popis výsledku anglicky

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

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

IN - Informatika

OECD FORD obor

—

Projekt

—

Návaznosti

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

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

International Journal of Bioscience, Biochemistry and Bioinformatics

ISSN

2010-3638

e-ISSN

—

Svazek periodika

6

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

18-25

Kód UT WoS článku

—

EID výsledku v databázi Scopus

—