Multiple 3D RNA Structure Superposition Using Neighbor Joining

Kód výsledku v IS VaVaI

RIV/60461373:22310/15:43900537 - isvavai.cz

Nalezeny alternativní kódy

RIV/00216208:11320/15:10275738

Výsledek na webu

http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6883172

DOI - Digital Object Identifier

10.1109/TCBB.2014.2351810

Jazyk výsledku

angličtina

Název v původním jazyce

Multiple 3D RNA Structure Superposition Using Neighbor Joining

Popis výsledku v původním jazyce

Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

Název v anglickém jazyce

Multiple 3D RNA Structure Superposition Using Neighbor Joining

Popis výsledku anglicky

Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

Druh

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

CEP obor

IN - Informatika

OECD FORD obor

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Projekt

GAP202/11/0968: Podobnostní nemetrické vyhledávání v rozsáhlých komplexních databázích

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2015

Kód důvěrnosti údajů

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

Název periodika

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

ISSN

1545-5963

e-ISSN

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Svazek periodika

12

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

520-530

Kód UT WoS článku

000359281500003

EID výsledku v databázi Scopus

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