Markov encoding for detecting signals in genomic sequences

Rajapakse J.C.; Loi Sy Ho

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Markov encoding for detecting signals in genomic sequences

机译：马尔可夫编码用于检测基因组序列中的信号

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We present a technique to encode the inputs to neural networks for the detection of signals in genomic sequences. The encoding is based on lower-order Markov models which incorporate known biological characteristics in genomic sequences. The neural networks then learn intrinsic higher-order dependencies of nucleotides at the signal sites. We demonstrate the efficacy of the Markov encoding method in the detection of three genomic signals, namely, splice sites, transcription start sites, and translation initiation sites.

机译：我们提出了一种对输入到神经网络的编码进行编码的技术，以检测基因组序列中的信号。编码基于低阶马尔可夫模型，该模型在基因组序列中结合了已知的生物学特征。然后，神经网络学习信号位点上核苷酸的内在高阶依赖性。我们证明了马尔可夫编码方法在检测三个基因组信号，即剪接位点，转录起始位点和翻译起始位点的功效。

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《IEEE/ACM transactions on computational biology and bioinformatics》 |2005年第2期|p.131-142|共12页
作者
Rajapakse J.C.; Loi Sy Ho;
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原文格式 PDF
正文语种 eng
中图分类生物数学方法;生物信息论;
关键词
Markov processes; biology computing; encoding; genetics; molecular biophysics; molecular configurations; neural nets; Markov encoding; genomic sequences; lower-order Markov models; neural networks; nucleotides; signal detection; splice sites; transcription start sites;

机译：马尔可夫过程;生物学计算;编码;遗传学;分子生物物理学;分子构型;神经网络;马尔可夫编码;基因组序列;低阶马尔可夫模型;神经网络;核苷酸;信号检测;剪接位点;转录起始位点;

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1. A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective [J] . Hyun-Seok Park Genomics & Informatics . 2018,第3期

机译：关于编码/广播ChromHMM注释200-BP基因组单位的DNA序列Markov属性的简短报告：计算视角
2. Detecting Ltr Structures In Human Genomic Sequences Usingrnprofile Hidden Markov Models [J] . Li, Ching Wu, Hsien, Expert systems with applications . 2009,第1期

机译：使用rnprofile隐马尔可夫模型检测人类基因组序列中的Ltr结构
3. Functional expression of the genomic DNA sequences encoding mouse Na,K-ATPase alpha 1 gene by cotransfection of overlapping genomic DNA segments. [J] . S Y Tam, E N Geissler, S L Graw, Molecular and Cellular Biology . 1990,第12期

机译：通过共转染重叠的基因组DNA片段，编码小鼠Na，K-ATPase alpha 1基因的基因组DNA序列的功能表达。
4. Geometric Encoding, Filtering, and Visualization of Genomic Sequences [C] . Helena Cristina da Gama Leitao, Rafael Felipe Veiga Saracchini, Jorge Stolfi International Conference on Information Visualization Theory and Applications . 2015

机译：基因组序列的几何编码，过滤和可视化
5. Jurassic limestone-marl sequences in Northern Spain: Detecting diagenetic signals using rare earth and trace elements. [D] . Hollon, Brittany Elise. 2012

机译：西班牙北部的侏罗纪石灰岩-泥灰岩序列：使用稀土和微量元素检测成岩信号。
6. A Short Report on the Markov Property of DNA Sequences on 200-bp Genomic Units of ENCODE/Broad ChromHMM Annotations: A Computational Perspective [O] . Hyun-Seok Park 2018

机译：关于编码/广泛的ChromHMM注释的200 bp基因组单元上DNA序列的马尔可夫性质的简短报告：计算视角
7. Markov encoding for detecting signals in genomic sequences [O] . Jagath C. Rajapakse, Loi Sy Ho 2010

机译：马尔可夫编码用于检测基因组序列中的信号

Markov encoding for detecting signals in genomic sequences

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