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OJBtm

Online Journal of Bioinformatics

Established 1995

ISSN  1443-2250

 

Volume 20(1):43-46, 2019.


A fast Fourier approach to model genomic elements.

 

Mahesh Yaragatti.

 

Biotechnology Program, University of Pennsylvania, Philadelphia, PA, 19104, USA

 

ABSTRACT

 

Yaragatti M., A fast Fourier approach to model genomic elements, Onl J Bioinform., 20(1):43-46, 2019. With hundreds of sequenced genomes readily available, a fundamental challenge is to identify, in particular, non-coding gene regulatory transcriptional elements. The importance of gene regulation is exemplified in pathological cell states such as cancer. Our prior work has involved the isolation of active regulatory fragments from cancer cells and the prediction of putative active sequences using a systems approach. Advancing that framework, we applied the fast Fourier transform (FFT) to predict possible active sequences from a random set. Our results clearly show differences in FFT scores between random and functional sequence vectors. The automation of this simple and fast approach could greatly complement an experimental system aimed at identifying transcriptional regulatory elements.

 

Keywords: Fourier, model, transcription, regulation, genome.


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