MersV1, Main, Exploration, bibRecord, 001186

KCMBT: a k-mer Counter based on Multiple Burst Trees.

Identifieur interne : 001186 ( Main/Exploration ); précédent : 001185; suivant : 001187

KCMBT: 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.

RBID : pubmed:27283950

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Biologie informatique (), Génome, Humains, Logiciel, Séquence nucléotidique.
MESH :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Biologie informatique, Génome, Humains, Logiciel, Séquence nucléotidique.

English descriptors

KwdEn :
- Algorithms, Base Sequence, Computational Biology (methods), Genome, Humans, Sequence Alignment, Sequence Analysis, DNA, Software.
MESH :
- methods : Computational Biology.
- Algorithms, Base Sequence, Genome, Humans, Sequence Alignment, Sequence Analysis, DNA, Software.

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:

Le 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>
<idno type="wicri:Area/Main/Merge">001190</idno>
<idno type="wicri:Area/Main/Curation">001186</idno>
<idno type="wicri:Area/Main/Exploration">001186</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/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001186 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001186 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |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/Main/Exploration/RBID.i   -Sk "pubmed:27283950" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

KCMBT: a k-mer Counter based on Multiple Burst Trees.

KCMBT: a k-mer Counter based on Multiple Burst Trees.

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

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.