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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.