PUBLICATION
Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish
- Authors
- Mishra, S.K., Wang, H.
- ID
- ZDB-PUB-210501-43
- Date
- 2021
- Source
- Biology 10(5): (Other)
- Registered Authors
- Wang, Han
- Keywords
- bioinformatics, coding probabilities, lncRNAs, zebrafish
- MeSH Terms
- none
- PubMed
- 33925925 Full text @ Biology (Basel)
Citation
Mishra, S.K., Wang, H. (2021) Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish. Biology. 10(5).
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping