MersV1, Main, Exploration, bibRecord, 003617

Spectrum alignment: efficient resequencing by hybridization.

Identifieur interne : 003617 ( Main/Exploration ); précédent : 003616; suivant : 003618

Spectrum alignment: efficient resequencing by hybridization.

Auteurs : I. Pe'Er [Israël] ; R. Shamir

Source :

Proceedings. International Conference on Intelligent Systems for Molecular Biology [ 1553-0833 ] ; 2000.

RBID : pubmed:10977087

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences (), Animaux, Chaines de Markov, Génome, Humains, Hybridation d'acides nucléiques, Séquençage par oligonucléotides en batterie.
MESH :
- Algorithmes, Alignement de séquences, Animaux, Chaines de Markov, Génome, Humains, Hybridation d'acides nucléiques, Séquençage par oligonucléotides en batterie.

English descriptors

KwdEn :
- Algorithms, Animals, Genome, Humans, Markov Chains, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Sequence Alignment (methods).
MESH :
- methods : Sequence Alignment.
- Algorithms, Animals, Genome, Humans, Markov Chains, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis.

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

Affiliations:

Israël

Le document en format XML

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<affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, Tel Aviv University, Israel. izik@math.tau.ac.il</nlm:affiliation>
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<wicri:noRegion>Tel Aviv University</wicri:noRegion>
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<term>Nucleic Acid Hybridization</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Sequence Alignment (methods)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
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<term>Markov Chains</term>
<term>Nucleic Acid Hybridization</term>
<term>Oligonucleotide Array Sequence Analysis</term>
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<term>Alignement de séquences</term>
<term>Animaux</term>
<term>Chaines de Markov</term>
<term>Génome</term>
<term>Humains</term>
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<front><div type="abstract" xml:lang="en">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.</div>
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Serveur d'exploration MERS

Spectrum alignment: efficient resequencing by hybridization.

Spectrum alignment: efficient resequencing by hybridization.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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