کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
559301 1451734 2015 9 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
A dynamic representation-based, de novo method for protein-coding region prediction and biological information detection
ترجمه فارسی عنوان
یک روش پویا مبتنی بر مشاهدات پویا برای پیش بینی منطقه پروتئین و تشخیص اطلاعات بیولوژیکی
موضوعات مرتبط
مهندسی و علوم پایه مهندسی کامپیوتر پردازش سیگنال
چکیده انگلیسی

In this paper, we propose a new method for the prediction of protein coding regions that is designed to detect novel genes that do not have known, close homologs. The proposed method uses a dynamic representation scheme to convert DNA sequences into a numerical form, and then it uses the nucleotide distribution variance to calculate the period-3 spectrum. The dynamic representation scheme assigns numerical pairs to the nucleotides to emphasize the effect of the nucleotides that have a stronger participation in the period-3 spectrum. The proposed method also uses the nucleotide distribution variance which has less computational cost than the Fourier transform to extract the period-3 spectrum. A post-processing of the period-3 spectrum signal is performed to smooth the signal, detect the period-3 spectrum peaks, and locate the boundaries of the protein-coding regions.The analysis of the receiver operating characteristic (ROC) curves shows that the proposed method outperforms other Digital Signal Processing (DSP)-based methods. The analysis of the false positive peaks shows that these regions have a similarity with regions that have functional patterns in other DNA sequences. The method also highlights and explores the capabilities of techniques that perform better than homology-based techniques for de novo protein prediction. We believe that this is an area of research that has been underemphasized and deserves additional attention.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Digital Signal Processing - Volume 46, November 2015, Pages 10–18
نویسندگان
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