MersV1, PubMed, Corpus, bibRecord, 001C29

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.

Identifieur interne : 001C29 ( PubMed/Corpus ); précédent : 001C28; suivant : 001C30

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.

Auteurs : David Williams ; William L. Trimble ; Meghan Shilts ; Folker Meyer ; Howard Ochman

Source :

BMC genomics [ 1471-2164 ] ; 2013.

RBID : pubmed:23924250

English descriptors

KwdEn :
- Escherichia coli (genetics), Gene Dosage (genetics), Genome Size, Genome, Bacterial (genetics), Genomics, Repetitive Sequences, Nucleic Acid (genetics), Sequence Analysis, Time Factors.
MESH :
- genetics : Escherichia coli, Gene Dosage, Genome, Bacterial, Repetitive Sequences, Nucleic Acid.
- Genome Size, Genomics, Sequence Analysis, Time Factors.

Abstract

The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.

DOI: 10.1186/1471-2164-14-537
PubMed: 23924250

Links to Exploration step

pubmed:23924250

Le document en format XML

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<author><name sortKey="Williams, David" sort="Williams, David" uniqKey="Williams D" first="David" last="Williams">David Williams</name>
<affiliation><nlm:affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Trimble, William L" sort="Trimble, William L" uniqKey="Trimble W" first="William L" last="Trimble">William L. Trimble</name>
</author>
<author><name sortKey="Shilts, Meghan" sort="Shilts, Meghan" uniqKey="Shilts M" first="Meghan" last="Shilts">Meghan Shilts</name>
</author>
<author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name>
</author>
<author><name sortKey="Ochman, Howard" sort="Ochman, Howard" uniqKey="Ochman H" first="Howard" last="Ochman">Howard Ochman</name>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.</title>
<author><name sortKey="Williams, David" sort="Williams, David" uniqKey="Williams D" first="David" last="Williams">David Williams</name>
<affiliation><nlm:affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</nlm:affiliation>
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<author><name sortKey="Trimble, William L" sort="Trimble, William L" uniqKey="Trimble W" first="William L" last="Trimble">William L. Trimble</name>
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<author><name sortKey="Shilts, Meghan" sort="Shilts, Meghan" uniqKey="Shilts M" first="Meghan" last="Shilts">Meghan Shilts</name>
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<author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name>
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<author><name sortKey="Ochman, Howard" sort="Ochman, Howard" uniqKey="Ochman H" first="Howard" last="Ochman">Howard Ochman</name>
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<series><title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2013" type="published">2013</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Escherichia coli (genetics)</term>
<term>Gene Dosage (genetics)</term>
<term>Genome Size</term>
<term>Genome, Bacterial (genetics)</term>
<term>Genomics</term>
<term>Repetitive Sequences, Nucleic Acid (genetics)</term>
<term>Sequence Analysis</term>
<term>Time Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term>
<term>Gene Dosage</term>
<term>Genome, Bacterial</term>
<term>Repetitive Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Genome Size</term>
<term>Genomics</term>
<term>Sequence Analysis</term>
<term>Time Factors</term>
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<front><div type="abstract" xml:lang="en">The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.</div>
</front>
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<DateCompleted><Year>2013</Year>
<Month>10</Month>
<Day>30</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>14</Volume>
<PubDate><Year>2013</Year>
<Month>Aug</Month>
<Day>08</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
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<ArticleTitle>Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.</ArticleTitle>
<Pagination><MedlinePgn>537</MedlinePgn>
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<ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-14-537</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Application of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Williams</LastName>
<ForeName>David</ForeName>
<Initials>D</Initials>
<AffiliationInfo><Affiliation>Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Trimble</LastName>
<ForeName>William L</ForeName>
<Initials>WL</Initials>
</Author>
<Author ValidYN="Y"><LastName>Shilts</LastName>
<ForeName>Meghan</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Meyer</LastName>
<ForeName>Folker</ForeName>
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<Author ValidYN="Y"><LastName>Ochman</LastName>
<ForeName>Howard</ForeName>
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<Language>eng</Language>
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<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D004926" MajorTopicYN="N">Escherichia coli</DescriptorName>
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<MeshHeading><DescriptorName UI="D018628" MajorTopicYN="N">Gene Dosage</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D059646" MajorTopicYN="Y">Genome Size</DescriptorName>
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<MeshHeading><DescriptorName UI="D016680" MajorTopicYN="N">Genome, Bacterial</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012091" MajorTopicYN="N">Repetitive Sequences, Nucleic Acid</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017421" MajorTopicYN="Y">Sequence Analysis</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D013997" MajorTopicYN="N">Time Factors</DescriptorName>
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<Month>04</Month>
<Day>26</Day>
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Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes.

Source :

English descriptors

Abstract

Links to Exploration step

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