IEEE J Biomed Health Inform - Identification of microsatellites in DNA using adaptive S-transform.

Tópicos

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Resumo

Microsatellites are tandem repeats of size 1-6 base pairs, associated with various diseases, DNA fingerprinting, and also useful in evolutionary studies. A signal processing algorithm for microsatellite detection, based on adaptive S-transform is proposed. The standard deviation of the Gaussian window kernel of the S-transform has been optimized for integer periods of interest by maximizing the concentration measure. The time-frequency plot is generated using optimal standard deviation values. Candidate repeats are marked by comparing the spectrogram values in the time-frequency plot with a threshold. A preprocessing phase followed by a verification phase extracts final results from the candidate repeats. Simulation studies on DNA sequences establish the superiority of this algorithm over other existing methods. Applicability of this algorithm in the analysis of DNA sequences associated with repeat expansion diseases has also been demonstrated.

Resumo Limpo

microsatellit tandem repeat size base pair associ various diseas dna fingerprint also use evolutionari studi signal process algorithm microsatellit detect base adapt stransform propos standard deviat gaussian window kernel stransform optim integ period interest maxim concentr measur timefrequ plot generat use optim standard deviat valu candid repeat mark compar spectrogram valu timefrequ plot threshold preprocess phase follow verif phase extract final result candid repeat simul studi dna sequenc establish superior algorithm exist method applic algorithm analysi dna sequenc associ repeat expans diseas also demonstr

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