Abstract
Background: MicroRNAs (miRNAs) are small noncoding RNAs which play crucial role in response to the adverse biotic and abiotic stress conditions at the post transcriptional level. The functions of the miRNAs are generally based on complementarity to their target region. Results: We used the online tool psRNA Target for the identification of submergence responsive miRNA using the gene expression profile related to the submergence condition. We wrote a perl script for the prediction of miRNA target gene. The position based feature of the script increases the overall specificity of the program. Our perl script performed well on the genomic data of Oryza sativa and produced significant results with their positions. These results were analyzed on the basis of complementarity and the statistical scores are used to find out the most probable binding regions. These predicted binding regions are aligned with their respective miRNAs to find out the consensus sequence. We scored the alignment using a position dependent, mismatch penalty system. We also identified the rate of conservation of bases at a particular position for all the predicted binding regions and it was found that all the predicted binding regions maintain above 70% rate of conservation of bases. Conclusion: Our approach provides a novel framework for screening the genome of Oryza sativa. It can be broadly applied to identify complementarity specific miRNA targets computationally by doing a little modification of the script depending on the type of the miRNA.
Highlights
MicroRNAs are small noncoding RNAs which play crucial role in response to the adverse biotic and abiotic stress conditions at the post transcriptional level
Before applying our perl script against the genomic data of Oryza sativa we first investigated whether our script gives true result with their exact position by using a small nucleotide sequence
It has been reported that miRNAs affect the expression of a number of target genes involved in different developmental processes and stresses. We expect that both the complementarity and the Genome-wide identification of submergence responsive miRNA targets Depending on the sequence information, perl script was written for each of these miRNAs to find out their binding position within the genome of Oryza sativa
Summary
MicroRNAs (miRNAs) are small noncoding RNAs which play crucial role in response to the adverse biotic and abiotic stress conditions at the post transcriptional level. Our perl script performed well on the genomic data of Oryza sativa and produced significant results with their positions These results were analyzed on the basis of complementarity and the statistical scores are used to find out the most probable binding regions. MicroRNAs (miRNAs) play significant role in response to the adverse biotic and abiotic stress conditions at the post-transcriptional level [7]. They are small, non-coding, single stranded RNAs that are abundantly found in prokaryotic and eukaryotic cells and can trigger
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
