Spectrum alignment: efficient resequencing by hybridization.
Identifieur interne : 002577 ( PubMed/Corpus ); précédent : 002576; suivant : 002578Spectrum alignment: efficient resequencing by hybridization.
Auteurs : I. Pe'Er ; R. ShamirSource :
- Proceedings. International Conference on Intelligent Systems for Molecular Biology [ 1553-0833 ] ; 2000.
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- MESH :
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.
PubMed: 10977087
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Shamir</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2000">2000</date><idno type="RBID">pubmed:10977087</idno><idno type="pmid">10977087</idno><idno type="wicri:Area/PubMed/Corpus">002577</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002577</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Spectrum alignment: efficient resequencing by hybridization.</title><author><name sortKey="Pe Er, I" sort="Pe Er, I" uniqKey="Pe Er I" first="I" last="Pe'Er">I. Pe'Er</name><affiliation><nlm:affiliation>Department of Computer Science, Tel Aviv University, Israel. izik@math.tau.ac.il</nlm:affiliation></affiliation></author><author><name sortKey="Shamir, R" sort="Shamir, R" uniqKey="Shamir R" first="R" last="Shamir">R. Shamir</name></author></analytic><series><title level="j">Proceedings. 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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. 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