Estimating the occurrence rate of DNA palindromes

NCU Institutional Repository > 理學院 > 統計研究所 > 期刊論文 > Item 987654321/105783

請使用永久網址來引用或連結此文件: https://ir.lib.ncu.edu.tw/handle/987654321/105783

題名:	Estimating the occurrence rate of DNA palindromes
作者:	王紹宣;Tu, I-Ping;Wang, Shao-Hsuan;Huang, Yuan-Fu
貢獻者:	理學院統計研究所
關鍵詞:	DNA;DNA palindrome;Estimation methods;genome sequence;Genomes;hairpin structure;higher order Markov model;hot-spot;Markov model;Markov models;Nucleotide sequences;occurrence rate;P values;p-value;Palindromes;Poisson process;power;Replication origin;segmented Markov model;Statistics
日期:	2013-06-01
上傳時間:	2026-04-23 12:53:00 (UTC+8)
出版者:	Institute of Mathematical Statistics
摘要:	摘要： A DNA palindrome is a segment of letters along a DNA sequence with inversion symmetry that one strand is identical to its complementary one running in the opposite direction. Searching nonrandom clusters of DNA palindromes, an interesting bioinformatic problem, relies on the estimation of the null palindrome occurrence rate. The most commonly used approach for estimating this number is the average rate method. However, we observed that the average rate could exceed the actual rate by 50% when inserting 5000 bp hotspot regions with 15-fold rate in a simulated 150,000 bp genome sequence. Here, we propose a Markov based estimator to avoid counting the number of palindromes directly, and thus to reduce the impact from the hot-spots. Our simulation shows that this method is more robust against the hot-spot effect than the average rate method. Furthermore, this method can be generalized to either a higher order Markov model or a segmented Markov model, and extended to calculate the occurrence rate for palindromes with gaps. We also provide a p-value approximation for various scan statistics to test nonrandom palindrome clusters under a Markov model. 出版者： Institute of Mathematical Statistics 出版日期： 2013-06-01 出處： The annals of applied statistics, 2013-06, Vol.7 (2), p.1095-1110 資源來源： JSTOR Arts and Sciences VII 版權： Copyright © 2013 Institute of Mathematical Statistics 版權： Copyright 2013 Institute of Mathematical Statistics 識別號： ISSN: 1932-6157 識別號： EISSN: 1941-7330 識別號： DOI: 10.1214/12-AOAS622
顯示於類別:	[統計研究所] 期刊論文

文件中的檔案:

檔案	描述	大小	格式	瀏覽次數
index.html		0Kb	HTML	13	檢視/開啟

在NCUIR中所有的資料項目都受到原著作權保護.

社群 sharing

資料載入中.....