Fast large scale oligonucleotide selection using the longest common factor approach.
Identifieur interne : 003219 ( Main/Exploration ); précédent : 003218; suivant : 003220Fast large scale oligonucleotide selection using the longest common factor approach.
Auteurs : Sven Rahmann [Allemagne]Source :
- Journal of bioinformatics and computational biology [ 0219-7200 ] ; 2003.
Descripteurs français
- KwdFr :
- Algorithmes, Alignement de séquences (), Analyse de profil d'expression de gènes (), Analyse de séquence d'ADN (), Conception assistée par ordinateur, Données de séquences moléculaires, Oligonucléotides (génétique), Oligonucléotides (synthèse chimique), Similitude de séquences d'acides nucléiques, Sondes oligonucléotidiques (génétique), Sondes oligonucléotidiques (synthèse chimique), Séquence nucléotidique, Séquençage par oligonucléotides en batterie ().
- MESH :
- génétique : Oligonucléotides, Sondes oligonucléotidiques.
- synthèse chimique : Oligonucléotides, Sondes oligonucléotidiques.
- Algorithmes, Alignement de séquences, Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Conception assistée par ordinateur, Données de séquences moléculaires, Similitude de séquences d'acides nucléiques, Séquence nucléotidique, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Algorithms, Base Sequence, Computer-Aided Design, Gene Expression Profiling (methods), Molecular Sequence Data, Oligonucleotide Array Sequence Analysis (methods), Oligonucleotide Probes (chemical synthesis), Oligonucleotide Probes (genetics), Oligonucleotides (chemical synthesis), Oligonucleotides (genetics), Sequence Alignment (methods), Sequence Analysis, DNA (methods), Sequence Homology, Nucleic Acid.
- MESH :
- chemical , chemical synthesis : Oligonucleotide Probes, Oligonucleotides.
- chemical , genetics : Oligonucleotide Probes, Oligonucleotides.
- methods : Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Sequence Alignment, Sequence Analysis, DNA.
- Algorithms, Base Sequence, Computer-Aided Design, Molecular Sequence Data, Sequence Homology, Nucleic Acid.
Abstract
We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within four days, a speedup of one to two orders of magnitude compared to previous approaches. This speed is attained by using the longest common substring as a specificity measure for candidate oligos. We present a space- and time-efficient algorithm, based on a suffix array with additional information, to compute matching statistics (lengths of longest matches) between all candidate oligos and all remaining sequences. With the matching statistics available, we show how to incorporate constraints such as oligo length, melting temperature, and self-complementarity into the selection process at a postprocessing stage. As a result, we can now design custom oligos for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.
DOI: 10.1142/s0219720003000125
PubMed: 15290776
Affiliations:
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Le document en format XML
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Sven.Rahmann@molgen.mpg.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2003">2003</date><idno type="RBID">pubmed:15290776</idno><idno type="pmid">15290776</idno><idno type="doi">10.1142/s0219720003000125</idno><idno type="wicri:Area/PubMed/Corpus">002375</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002375</idno><idno type="wicri:Area/PubMed/Curation">002375</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002375</idno><idno type="wicri:Area/PubMed/Checkpoint">002324</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002324</idno><idno type="wicri:Area/Ncbi/Merge">000296</idno><idno type="wicri:Area/Ncbi/Curation">000296</idno><idno type="wicri:Area/Ncbi/Checkpoint">000296</idno><idno type="wicri:doubleKey">0219-7200:2003:Rahmann S:fast:large:scale</idno><idno type="wicri:Area/Main/Merge">003254</idno><idno type="wicri:Area/Main/Curation">003219</idno><idno type="wicri:Area/Main/Exploration">003219</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Fast large scale oligonucleotide selection using the longest common factor approach.</title><author><name sortKey="Rahmann, Sven" sort="Rahmann, Sven" uniqKey="Rahmann S" first="Sven" last="Rahmann">Sven Rahmann</name><affiliation wicri:level="3"><nlm:affiliation>Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany. Sven.Rahmann@molgen.mpg.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></analytic><series><title level="j">Journal of bioinformatics and computational biology</title><idno type="ISSN">0219-7200</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Base Sequence</term><term>Computer-Aided Design</term><term>Gene Expression Profiling (methods)</term><term>Molecular Sequence Data</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes (chemical synthesis)</term><term>Oligonucleotide Probes (genetics)</term><term>Oligonucleotides (chemical synthesis)</term><term>Oligonucleotides (genetics)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences ()</term><term>Analyse de profil d'expression de gènes ()</term><term>Analyse de séquence d'ADN ()</term><term>Conception assistée par ordinateur</term><term>Données de séquences moléculaires</term><term>Oligonucléotides (génétique)</term><term>Oligonucléotides (synthèse chimique)</term><term>Similitude de séquences d'acides nucléiques</term><term>Sondes oligonucléotidiques (génétique)</term><term>Sondes oligonucléotidiques (synthèse chimique)</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>Oligonucleotide Probes</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotide Probes</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Oligonucléotides</term><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Oligonucleotide Array Sequence Analysis</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="synthèse chimique" xml:lang="fr"><term>Oligonucléotides</term><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Base Sequence</term><term>Computer-Aided Design</term><term>Molecular Sequence Data</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ADN</term><term>Conception assistée par ordinateur</term><term>Données de séquences moléculaires</term><term>Similitude de séquences d'acides nucléiques</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within four days, a speedup of one to two orders of magnitude compared to previous approaches. This speed is attained by using the longest common substring as a specificity measure for candidate oligos. We present a space- and time-efficient algorithm, based on a suffix array with additional information, to compute matching statistics (lengths of longest matches) between all candidate oligos and all remaining sequences. With the matching statistics available, we show how to incorporate constraints such as oligo length, melting temperature, and self-complementarity into the selection process at a postprocessing stage. As a result, we can now design custom oligos for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.</div></front></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Berlin</li></region><settlement><li>Berlin</li></settlement></list><tree><country name="Allemagne"><region name="Berlin"><name sortKey="Rahmann, Sven" sort="Rahmann, Sven" uniqKey="Rahmann S" first="Sven" last="Rahmann">Sven Rahmann</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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