Fast genotyping of known SNPs through approximate k-mer matching.
Identifieur interne : 001257 ( Main/Merge ); précédent : 001256; suivant : 001258Fast genotyping of known SNPs through approximate k-mer matching.
Auteurs : Ariya Shajii [États-Unis] ; Deniz Yorukoglu ; Yun William Yu [États-Unis] ; Bonnie Berger [États-Unis]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
As the volume of next-generation sequencing (NGS) data increases, faster algorithms become necessary. Although speeding up individual components of a sequence analysis pipeline (e.g. read mapping) can reduce the computational cost of analysis, such approaches do not take full advantage of the particulars of a given problem. One problem of great interest, genotyping a known set of variants (e.g. dbSNP or Affymetrix SNPs), is important for characterization of known genetic traits and causative disease variants within an individual, as well as the initial stage of many ancestral and population genomic pipelines (e.g. GWAS).
DOI: 10.1093/bioinformatics/btw460
PubMed: 27587672
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000F79
- to stream PubMed, to step Curation: 000F79
- to stream PubMed, to step Checkpoint: 001099
- to stream Ncbi, to step Merge: 001765
- to stream Ncbi, to step Curation: 001765
- to stream Ncbi, to step Checkpoint: 001765
Links to Exploration step
pubmed:27587672Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Fast genotyping of known SNPs through approximate k-mer matching.</title><author><name sortKey="Shajii, Ariya" sort="Shajii, Ariya" uniqKey="Shajii A" first="Ariya" last="Shajii">Ariya Shajii</name><affiliation wicri:level="2"><nlm:affiliation>Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Yorukoglu, Deniz" sort="Yorukoglu, Deniz" uniqKey="Yorukoglu D" first="Deniz" last="Yorukoglu">Deniz Yorukoglu</name><affiliation><nlm:affiliation>Computer Science and AI Lab.</nlm:affiliation><wicri:noCountry code="no comma">Computer Science and AI Lab.</wicri:noCountry></affiliation></author><author><name sortKey="William Yu, Yun" sort="William Yu, Yun" uniqKey="William Yu Y" first="Yun" last="William Yu">Yun William Yu</name><affiliation wicri:level="2"><nlm:affiliation>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Berger, Bonnie" sort="Berger, Bonnie" uniqKey="Berger B" first="Bonnie" last="Berger">Bonnie Berger</name><affiliation wicri:level="2"><nlm:affiliation>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27587672</idno><idno type="pmid">27587672</idno><idno type="doi">10.1093/bioinformatics/btw460</idno><idno type="wicri:Area/PubMed/Corpus">000F79</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000F79</idno><idno type="wicri:Area/PubMed/Curation">000F79</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000F79</idno><idno type="wicri:Area/PubMed/Checkpoint">001099</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001099</idno><idno type="wicri:Area/Ncbi/Merge">001765</idno><idno type="wicri:Area/Ncbi/Curation">001765</idno><idno type="wicri:Area/Ncbi/Checkpoint">001765</idno><idno type="wicri:Area/Main/Merge">001257</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Fast genotyping of known SNPs through approximate k-mer matching.</title><author><name sortKey="Shajii, Ariya" sort="Shajii, Ariya" uniqKey="Shajii A" first="Ariya" last="Shajii">Ariya Shajii</name><affiliation wicri:level="2"><nlm:affiliation>Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Yorukoglu, Deniz" sort="Yorukoglu, Deniz" uniqKey="Yorukoglu D" first="Deniz" last="Yorukoglu">Deniz Yorukoglu</name><affiliation><nlm:affiliation>Computer Science and AI Lab.</nlm:affiliation><wicri:noCountry code="no comma">Computer Science and AI Lab.</wicri:noCountry></affiliation></author><author><name sortKey="William Yu, Yun" sort="William Yu, Yun" uniqKey="William Yu Y" first="Yun" last="William Yu">Yun William Yu</name><affiliation wicri:level="2"><nlm:affiliation>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Berger, Bonnie" sort="Berger, Bonnie" uniqKey="Berger B" first="Bonnie" last="Berger">Bonnie Berger</name><affiliation wicri:level="2"><nlm:affiliation>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and AI Lab Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Alleles</term><term>Cluster Analysis</term><term>Genome, Human</term><term>Genotype</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Allèles</term><term>Analyse de regroupements</term><term>Génome humain</term><term>Génotype</term><term>Humains</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Alleles</term><term>Cluster Analysis</term><term>Genome, Human</term><term>Genotype</term><term>Humans</term><term>Polymorphism, Single Nucleotide</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Allèles</term><term>Analyse de regroupements</term><term>Génome humain</term><term>Génotype</term><term>Humains</term><term>Logiciel</term><term>Polymorphisme de nucléotide simple</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As the volume of next-generation sequencing (NGS) data increases, faster algorithms become necessary. Although speeding up individual components of a sequence analysis pipeline (e.g. read mapping) can reduce the computational cost of analysis, such approaches do not take full advantage of the particulars of a given problem. One problem of great interest, genotyping a known set of variants (e.g. dbSNP or Affymetrix SNPs), is important for characterization of known genetic traits and causative disease variants within an individual, as well as the initial stage of many ancestral and population genomic pipelines (e.g. GWAS).</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001257 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 001257 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Merge
|type= RBID
|clé= pubmed:27587672
|texte= Fast genotyping of known SNPs through approximate k-mer matching.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:27587672" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |