Cumulative Spectral Repeat Finder (CSRF): A Spectral Approach for Identifying the Length of Repeats in DNA Sequences

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题名:	Cumulative Spectral Repeat Finder (CSRF): A Spectral Approach for Identifying the Length of Repeats in DNA Sequences
作者:	蔡進發;Jeffrey, J.P.Tsai
贡献者:	生物與醫學資訊學系
关键词:	DNA sequence;repetitive sequence;spectral analysis
日期:	2011
上传时间:	2012-11-23 09:15:21 (UTC+0)
摘要:	Repetitive sequences of DNA are meaningful and of great importance to human functions. Previous researchers have proposed various methods to discover repetitive sequences in DNA sequence. However, the unknown lengths for repetitive sequences are usually predicted randomly or determined by rules of thumb rather than using a systematical criterion. We propose a new algorithm based on the cumulative Fourier spectral contents of DNA sequence to identify the candidate lengths of repetitive sequences or repeats in DNA sequences. After the candidate lengths of repeats are known, one can identify the repeats and their copy numbers using an exact method. Both of the simulated and real datasets are used to illustrate the performance of the proposed algorithm. The results are also compared to two well-known methods such as Spectral Repeat Finder (SRF) and Gibbs sampler. Furthermore, we demonstrate the use of CSRF in some well-known repeats-finding methods such as SRF, Gibbs sampler, MEME. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0218213011000073
關聯:	International Journal on Artificial Intelligence Tools
显示于类别:	[生物資訊與醫學工程學系 ] 期刊論文

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