Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish
Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA...
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doaj-2d1ad1516a074e2cb1b35a023c8ac9852021-04-26T23:02:26ZengMDPI AGBiology2079-77372021-04-011037137110.3390/biology10050371Computational Analysis Predicts Hundreds of Coding lncRNAs in ZebrafishShital Kumar Mishra0Han Wang1Center for Circadian Clocks, Soochow University, Suzhou 215123, ChinaCenter for Circadian Clocks, Soochow University, Suzhou 215123, ChinaRecent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies.https://www.mdpi.com/2079-7737/10/5/371lncRNAscoding probabilitiesbioinformaticszebrafish |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shital Kumar Mishra Han Wang |
spellingShingle |
Shital Kumar Mishra Han Wang Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish Biology lncRNAs coding probabilities bioinformatics zebrafish |
author_facet |
Shital Kumar Mishra Han Wang |
author_sort |
Shital Kumar Mishra |
title |
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish |
title_short |
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish |
title_full |
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish |
title_fullStr |
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish |
title_full_unstemmed |
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish |
title_sort |
computational analysis predicts hundreds of coding lncrnas in zebrafish |
publisher |
MDPI AG |
series |
Biology |
issn |
2079-7737 |
publishDate |
2021-04-01 |
description |
Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies. |
topic |
lncRNAs coding probabilities bioinformatics zebrafish |
url |
https://www.mdpi.com/2079-7737/10/5/371 |
work_keys_str_mv |
AT shitalkumarmishra computationalanalysispredictshundredsofcodinglncrnasinzebrafish AT hanwang computationalanalysispredictshundredsofcodinglncrnasinzebrafish |
_version_ |
1721507275350212608 |