MersV1, Main, Exploration, bibRecord, 003316

Rapid large-scale oligonucleotide selection for microarrays.

Identifieur interne : 003316 ( Main/Exploration ); précédent : 003315; suivant : 003317

Rapid large-scale oligonucleotide selection for microarrays.

Auteurs : Sven Rahmann [Allemagne]

Source :

Proceedings. IEEE Computer Society Bioinformatics Conference [ 1555-3930 ] ; 2002.

RBID : pubmed:15838123

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences (), Analyse de séquence d'ADN (), Données de séquences moléculaires, Sondes oligonucléotidiques (génétique), Séquence nucléotidique, Séquençage par oligonucléotides en batterie ().
MESH :
- génétique : Sondes oligonucléotidiques.
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Données de séquences moléculaires, Séquence nucléotidique, Séquençage par oligonucléotides en batterie.

English descriptors

KwdEn :
- Algorithms, Base Sequence, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotide Probes (genetics), Sequence Alignment (methods), Sequence Analysis, DNA (methods).
MESH :
- chemical , genetics : Oligonucleotide Probes.
- methods : Oligonucleotide Array Sequence Analysis, Sequence Alignment, Sequence Analysis, DNA.
- Algorithms, Base Sequence, Molecular Sequence Data.

Abstract

We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This becomes possible by using the longest common substring as a specificity measure for candidate oligos. We present an algorithm based on a suffix array with additional information that is efficient both in terms of memory usage and running time to rank all candidate oligos according to their specificity. We also introduce the concept of master sequences to describe the sequences from which oligos are to be selected. Constraints such as oligo length, melting temperature, and self-complementarity are incorporated in the master sequence at a preprocessing stage and thus kept separate from the main selection problem. As a result, custom oligos can now be designed for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.

PubMed: 15838123

Affiliations:

Le document en format XML

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<affiliation wicri:level="3"><nlm:affiliation>Computational Molecular Biology, MPI for Molecular Genetics, Dept. of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany. Sven.Rahmann@molgen.mpg.de</nlm:affiliation>
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<term>Oligonucleotide Probes (genetics)</term>
<term>Sequence Alignment (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
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<term>Données de séquences moléculaires</term>
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<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Molecular Sequence Data</term>
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<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Données de séquences moléculaires</term>
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<front><div type="abstract" xml:lang="en">We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This becomes possible by using the longest common substring as a specificity measure for candidate oligos. We present an algorithm based on a suffix array with additional information that is efficient both in terms of memory usage and running time to rank all candidate oligos according to their specificity. We also introduce the concept of master sequences to describe the sequences from which oligos are to be selected. Constraints such as oligo length, melting temperature, and self-complementarity are incorporated in the master sequence at a preprocessing stage and thus kept separate from the main selection problem. As a result, custom oligos can now be designed for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.</div>
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Serveur d'exploration MERS

Rapid large-scale oligonucleotide selection for microarrays.

Rapid large-scale oligonucleotide selection for microarrays.

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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