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Comb Chem High Throughput Screen. 2019 Nov 28. doi: 10.2174/1386207322666191129112433. [Epub ahead of print]

A Spectral Rotation Method with Triplet Periodicity Property for Planted Motif Finding Problems.

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College of Computer and Communication Engineering, China University of Petroleum, Qingdao 266580, China.



Genes are known as functional patterns in genome and presumed to have biological significance. They can indicate binding sites for transcription factors and encoding certain proteins. Finding genes from biological sequences is a major task in computational biology for unraveling the mechanisms of gene expression.


Planted motif finding problems are a class of mathematical models abstracted from the process of detecting genes from genome, in which is a specific gene with a number of mutations is planted into a randomly generated background sequence, and then gene finding algorithms can be tested by check if the planted gene can be found in feasible time.


In this work, a spectral rotation method based on triplet periodicity property is obtained to solve planted motif finding problems.


The proposed method is with significant tolerance of base mutations in genes. Specifically, genes having a number of substitutions can be detected from randomly generated background sequences. Experimental results on genomic data set from Saccharomyces S. Cerevisiae reveal that genes can be visually distinguished. It is obtained that genes with about 50% mutations of gene can be detected from randomly generated background sequences.


It is found that with about 5 insertions or deletions, our method fails in finding the planted genes. For particular case, if the deletion of bases are located at the beginning of the gene, that is, bases are not randomly deleted, then the tolerance of the method for base deletion is increased.


Fast algorithm; Fourier spectrums; Gene detection; Motif finding; Planted motif finding problem; Visualization method

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