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Bioimpacts. 2018;8(1): 13-22.
doi: 10.15171/bi.2018.03
PMID: 29713598
PMCID: PMC5915704
Scopus ID: 85044295205
  Abstract View: 2196
  PDF Download: 1058
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Original Research

Development of a new sequential block finding strategy for detection of conserved sequences in riboswitches

Faegheh Golabi, Mousa Shamsi*, Mohammad Hosein Sedaaghi, Abolfazl Barzegar, Mohammad Saeid Hejazi*

1 Genomic Signal Processing Laboratory, Faculty of Electrical Engineering, Sahand University of Technology, Tabriz, Iran
2 School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
3 Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
4 Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
5 Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
*Corresponding Authors: Email: shamsi@sut.ac.ir; Email: msaeidhejazi@yahoo.com

Abstract

Introduction: Some non-coding RNAs have an important role in the regulation of gene expression and consequently cellular function. Riboswitches are examples of these regulatory RNAs. Riboswitches are classified into various families according to sequential and structural similarities.

Methods: In this study, a block finder algorithm for identification of frequently appearing sequential blocks in five families of riboswitches from Rfam 12.0 database, without the use of alignment methods, was developed.

Results: The developed program identified 21 frequently appearing blocks in five families of riboswitches.

Conclusion: Comparison of the results of the proposed algorithm with those of sequential alignment methods revealed that our method can recognize most of the patterns present in conserved areas of individual riboswitch families and determine them as specific blocks, implying potential of the developed program as a platform for further studies and developments.


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Submitted: 11 Dec 2016
Revision: 01 May 2017
Accepted: 08 Jul 2017
ePublished: 30 Aug 2017
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