rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F20%3A00532087" target="_blank" >RIV/61388971:_____/20:00532087 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.frontiersin.org/articles/10.3389/fgene.2020.00675/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fgene.2020.00675/full</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fgene.2020.00675" target="_blank" >10.3389/fgene.2020.00675</a>

Jazyk výsledku

angličtina

Název v původním jazyce

rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

Popis výsledku v původním jazyce

Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due to the presence of partial matches to the database subject sequences. Here, we present rboAnalyzer - a tool that helps with interpreting sequence search result by (1) extending partial matches into plausible full-length subject sequences, (2) predicting homology of RNAs represented by full-length subject sequences to the query RNA, (3) pooling information across homologous RNAs found in the search results and public databases such as Rfam to predict more reliable secondary structures for all matches, and (4) contextualizing the matches by providing the prediction results and other relevant information in a rich graphical output. Using predicted full-length matches improves secondary structure prediction and makes rboAnalyzer robust with regards to identification of homology. The output of the tool should help the user to reliably characterize non-coding RNAs in BLAST output. The usefulness of the rboAnalyzer and its ability to correctly extend partial matches to full-length is demonstrated on known homologous RNAs. To allow the user to use custom databases and search options, rboAnalyzer accepts any search results as a text file in the BLAST format. The main output is an interactive HTML page displaying the computed characteristics and other context of the matches. The output can also be exported in an appropriate sequence and/or secondary structure formats.

Název v anglickém jazyce

rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

Popis výsledku anglicky

Searching for similar sequences in a database via BLAST or a similar tool is one of the most common bioinformatics tasks applied in general, and to non-coding RNAs in particular. However, the results of the search might be difficult to interpret due to the presence of partial matches to the database subject sequences. Here, we present rboAnalyzer - a tool that helps with interpreting sequence search result by (1) extending partial matches into plausible full-length subject sequences, (2) predicting homology of RNAs represented by full-length subject sequences to the query RNA, (3) pooling information across homologous RNAs found in the search results and public databases such as Rfam to predict more reliable secondary structures for all matches, and (4) contextualizing the matches by providing the prediction results and other relevant information in a rich graphical output. Using predicted full-length matches improves secondary structure prediction and makes rboAnalyzer robust with regards to identification of homology. The output of the tool should help the user to reliably characterize non-coding RNAs in BLAST output. The usefulness of the rboAnalyzer and its ability to correctly extend partial matches to full-length is demonstrated on known homologous RNAs. To allow the user to use custom databases and search options, rboAnalyzer accepts any search results as a text file in the BLAST format. The main output is an interactive HTML page displaying the computed characteristics and other context of the matches. The output can also be exported in an appropriate sequence and/or secondary structure formats.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název periodika

Frontiers in genetics

ISSN

1664-8021

e-ISSN

—

Svazek periodika

11

Číslo periodika v rámci svazku

Jul 28

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

13

Strana od-do

675

Kód UT WoS článku

000561398800001

EID výsledku v databázi Scopus

2-s2.0-85089337872