Title

Prediction of miRNA binding sites in mRNA

Authors

Anatoly Ivashchenko, Anna Pyrkova, Raigul Niyazova*, Aigul Alybayeva, Kirill Baskakov

Affiliation

Computer Science Laboratory, Al-Farabi Kazakh National University, Almaty - 050038, Kazakhstan,

Email

Raigul Niyazova – Email: raiguln@mail.ru, *Corresponding author

Article Type

Prediction Model

Date

Recieved May 26, 2016; Revised July 4, 2016; Accepted July 4, 2016; Published July 26, 2016

In the present article, a solution for the problem of gene scanning for the purpose of prediction of binding sites of miRNA with matrix RNA (mRNA) is proposed. A mathematical model for the optimal process of scanning of genes and miRNA sequences was developed. An algorithm for scanning of genes using miRNA with one gap in the miRNA sequence and maximum (as a percentage ratio) free
energy was developed and analysed with regard to the coincidence of miRNA and particular gene sites on the basis of complementarity. The constructed algorithm for scanning of genes using miRNA was parallelised and fragmented on the computational cluster with the use of MPJ tools.

Keywords

parallelized algorithm, cluster computing platform, Java MPI, miRNA, mRNA

Citation

Ivashchenko et al. Bioinformation 12(4): 237-240 (2016)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.