KCMBT: a k-mer Counter based on Multiple Burst Trees.
Identifieur interne : 001656 ( Ncbi/Merge ); 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.
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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
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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><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">27283950</PMID><DateCompleted><Year>2017</Year><Month>07</Month><Day>31</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>32</Volume><Issue>18</Issue><PubDate><Year>2016</Year><Month>09</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>KCMBT: a k-mer Counter based on Multiple Burst Trees.</ArticleTitle><Pagination><MedlinePgn>2783-90</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btw345</ELocationID><Abstract><AbstractText Label="MOTIVATION">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.</AbstractText><AbstractText Label="RESULTS">We propose a novel trie-based algorithm for this k-mer counting problem. We compare our devised algorithm k-mer Counter based on Multiple Burst Trees (KCMBT) with available all well-known algorithms. Our experimental results show that KCMBT is around 30% faster than the previous best-performing algorithm KMC2 for human genome dataset. As another example, our algorithm is around six times faster than Jellyfish2. Overall, KCMBT is 20-30% faster than KMC2 on five benchmark data sets when both the algorithms were run using multiple threads.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION">KCMBT is freely available on GitHub: (https://github.com/abdullah009/kcmbt_mt).</AbstractText><AbstractText Label="CONTACT">rajasek@engr.uconn.edu</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mamun</LastName><ForeName>Abdullah-Al</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pal</LastName><ForeName>Soumitra</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rajasekaran</LastName><ForeName>Sanguthevar</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList 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IdType="pubmed">12529310</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><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)
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