Identification of RNA pseudouridine sites using deep learning approaches

Abu Zahid Bin Aziz, Md Al Mehedi Hasan and Jungpil Shin

PLOS ONE, 2021, vol. 16, issue 2, 1-13

Abstract: Pseudouridine(Ψ) is widely popular among various RNA modifications which have been confirmed to occur in rRNA, mRNA, tRNA, and nuclear/nucleolar RNA. Hence, identifying them has vital significance in academic research, drug development and gene therapies. Several laboratory techniques for Ψ identification have been introduced over the years. Although these techniques produce satisfactory results, they are costly, time-consuming and requires skilled experience. As the lengths of RNA sequences are getting longer day by day, an efficient method for identifying pseudouridine sites using computational approaches is very important. In this paper, we proposed a multi-channel convolution neural network using binary encoding. We employed k-fold cross-validation and grid search to tune the hyperparameters. We evaluated its performance in the independent datasets and found promising results. The results proved that our method can be used to identify pseudouridine sites for associated purposes. We have also implemented an easily accessible web server at http://103.99.176.239/ipseumulticnn/.

Date: 2021
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0247511 (text/html)
https://journals.plos.org/plosone/article/file?id= ... 47511&type=printable (application/pdf)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0247511

DOI: 10.1371/journal.pone.0247511

Access Statistics for this article

More articles in PLOS ONE from Public Library of Science
Bibliographic data for series maintained by plosone ().