Spectrum alignment: efficient resequencing by hybridization.

I Pe'er; R Shamir

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PubMed · 10977087

Spectrum alignment: efficient resequencing by hybridization.

I Pe'er·R Shamir

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Abstract

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 homologue 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 2,000 nucleotides when a polymorphic sequence is known. The technique is generalized to handle profiles and HMMs as input instead of a single homologous sequence.

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Algorithms Animals Genome Humans Markov Chains Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Sequence Alignment Journal Article Research Support, Non-U.S. Gov't

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I Pe'er, R Shamir. 2000. Spectrum alignment: efficient resequencing by hybridization.. https://pubmed.ncbi.nlm.nih.gov/10977087/

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