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

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.