KCMBT: a k-mer Counter based on Multiple Burst Trees.
Identifieur interne : 001656 ( Ncbi/Checkpoint ); précédent : 001655; suivant : 001657KCMBT: a k-mer Counter based on Multiple Burst Trees.
Auteurs : Abdullah-Al Mamun [États-Unis] ; Soumitra Pal [États-Unis] ; Sanguthevar Rajasekaran [États-Unis]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
A massive number of bioinformatics applications require counting of k-length substrings in genetically important long strings. A k-mer counter generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection and many other related applications use a k-mer counter as a building block. Very fast and efficient algorithms are necessary to count k-mers in large data sets to be useful in such applications.
DOI: 10.1093/bioinformatics/btw345
PubMed: 27283950
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 001088
- to stream PubMed, to step Curation: 001088
- to stream PubMed, to step Checkpoint: 001037
- to stream Ncbi, to step Merge: 001656
- to stream Ncbi, to step Curation: 001656
Links to Exploration step
pubmed:27283950Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">KCMBT: a k-mer Counter based on Multiple Burst Trees.</title>
<author><name sortKey="Mamun, Abdullah Al" sort="Mamun, Abdullah Al" uniqKey="Mamun A" first="Abdullah-Al" last="Mamun">Abdullah-Al Mamun</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pal, Soumitra" sort="Pal, Soumitra" uniqKey="Pal S" first="Soumitra" last="Pal">Soumitra Pal</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Rajasekaran, Sanguthevar" sort="Rajasekaran, Sanguthevar" uniqKey="Rajasekaran S" first="Sanguthevar" last="Rajasekaran">Sanguthevar Rajasekaran</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2016">2016</date>
<idno type="RBID">pubmed:27283950</idno>
<idno type="pmid">27283950</idno>
<idno type="doi">10.1093/bioinformatics/btw345</idno>
<idno type="wicri:Area/PubMed/Corpus">001088</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001088</idno>
<idno type="wicri:Area/PubMed/Curation">001088</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001088</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001037</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001037</idno>
<idno type="wicri:Area/Ncbi/Merge">001656</idno>
<idno type="wicri:Area/Ncbi/Curation">001656</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001656</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">KCMBT: a k-mer Counter based on Multiple Burst Trees.</title>
<author><name sortKey="Mamun, Abdullah Al" sort="Mamun, Abdullah Al" uniqKey="Mamun A" first="Abdullah-Al" last="Mamun">Abdullah-Al Mamun</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pal, Soumitra" sort="Pal, Soumitra" uniqKey="Pal S" first="Soumitra" last="Pal">Soumitra Pal</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Rajasekaran, Sanguthevar" sort="Rajasekaran, Sanguthevar" uniqKey="Rajasekaran S" first="Sanguthevar" last="Rajasekaran">Sanguthevar Rajasekaran</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269</wicri:regionArea>
<placeName><region type="state">Connecticut</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>Base Sequence</term>
<term>Computational Biology (methods)</term>
<term>Genome</term>
<term>Humans</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Biologie informatique ()</term>
<term>Génome</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Séquence nucléotidique</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Base Sequence</term>
<term>Genome</term>
<term>Humans</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
<term>Software</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term>
<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Biologie informatique</term>
<term>Génome</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Séquence nucléotidique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">A massive number of bioinformatics applications require counting of k-length substrings in genetically important long strings. A k-mer counter generates the frequencies of each k-length substring in genome sequences. Genome assembly, repeat detection, multiple sequence alignment, error detection and many other related applications use a k-mer counter as a building block. Very fast and efficient algorithms are necessary to count k-mers in large data sets to be useful in such applications.</div>
</front>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Connecticut</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Connecticut"><name sortKey="Mamun, Abdullah Al" sort="Mamun, Abdullah Al" uniqKey="Mamun A" first="Abdullah-Al" last="Mamun">Abdullah-Al Mamun</name>
</region>
<name sortKey="Pal, Soumitra" sort="Pal, Soumitra" uniqKey="Pal S" first="Soumitra" last="Pal">Soumitra Pal</name>
<name sortKey="Rajasekaran, Sanguthevar" sort="Rajasekaran, Sanguthevar" uniqKey="Rajasekaran S" first="Sanguthevar" last="Rajasekaran">Sanguthevar Rajasekaran</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001656 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 001656 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Ncbi |étape= Checkpoint |type= RBID |clé= pubmed:27283950 |texte= KCMBT: a k-mer Counter based on Multiple Burst Trees. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:27283950" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |