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

Result code in 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>

Result on the web

<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>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

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

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

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

Name of the periodical

Frontiers in genetics

ISSN

1664-8021

e-ISSN

—

Volume of the periodical

11

Issue of the periodical within the volume

Jul 28

Country of publishing house

CH - SWITZERLAND

Number of pages

13

Pages from-to

675

UT code for WoS article

000561398800001

EID of the result in the Scopus database

2-s2.0-85089337872