Spectrum Alignment: Efficient Resequencing by Hybridization

扫码查看

原文链接

NETL

外文摘要：Recent high-density microarray technologies allow, in principle, the determination of all k-mers that appear along a DNA sequence, for k = 8 - 10 in a single experiment on a standard chip. The k-mer contents, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. We have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and a homologous sequence. This situation occurs, for example, in the identification of single nucleotide polymorphisms (SNPs), and whenever a homo-logue of the target sequence is known. The algorithm is robust, can handle errors in the spectrum and assumes no knowledge of the k-mer multiplicities. Our simulations show that with realistic levels of SNPs, the algorithm correctly reconstructs a target sequence of length up to 2000 nucleotides when a polymorphic sequence is known. The technique is generalized to handle profiles and HMMs as input instead of a single homologous sequence.

外文关键词：

sequencing by hybridizationmutation detectionSNP genotypinghidden markov modelsDNA Microarrays

作者：

I. Pe'er、R. Shamir

展开 >

作者单位：

Department of Computer Science, Tel Aviv University, Tel Aviv, 69978 ISRAEL

会议名称：

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology

会议地点：

La Jolla,CA(US)

会议母体文献：

International Conference on Intelligent Systems for Molecular Biology; 20000816-23; La Jolla,CA(US)

页码：

P.260-268

出版时间：

2000