Comput Biol Chem - Comparative analysis of periodicity search methods in DNA sequences.

Tópicos

{ signal(2180) analysi(812) frequenc(800) }
{ method(1219) similar(1157) match(930) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1557) propos(1049) approach(1037) }
{ intervent(3218) particip(2042) group(1664) }
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{ take(945) account(800) differ(722) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
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{ can(981) present(881) function(850) }
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Resumo

To determine the periodicity of a DNA sequence, different spectral approaches are applied (discrete Fourier transform (DFT), autocorrelation (CORR), information decomposition (ID), hybrid method (HYB), concept of spectral envelope for spectral analysis (SE), normalized autocorrelation (CORR_N) and profile analysis (PA). In this work, we investigated the possibility of finding the true period length, by depending on the average number of accumulated changes in DNA bases (PM) for the methods stated above. The results show that for periods with short length (=4 b.p), it is possible to use the hybrid method (HYB), which combines properties of autocorrelation, Fourier transform, and information decomposition (ID). For larger period lengths (>4) with values of point mutation (PM) equal to 1.0 or more per one nucleotide, it is preferable to use information of decomposition method (ID), as the other spectral approaches cannot achieve correct determination of the period length present in the analyzed sequence.

Resumo Limpo

determin period dna sequenc differ spectral approach appli discret fourier transform dft autocorrel corr inform decomposit id hybrid method hyb concept spectral envelop spectral analysi se normal autocorrel corrn profil analysi pa work investig possibl find true period length depend averag number accumul chang dna base pm method state result show period short length bp possibl use hybrid method hyb combin properti autocorrel fourier transform inform decomposit id larger period length valu point mutat pm equal per one nucleotid prefer use inform decomposit method id spectral approach achiev correct determin period length present analyz sequenc

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