SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.
Identifieur interne : 001A11 ( PubMed/Corpus ); précédent : 001A10; suivant : 001A12SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.
Auteurs : Kamil S. Jaron ; Ji C. Moravec ; Natália MartínkováSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- genetics : Eukaryota.
- methods : Genomics, Sequence Analysis, DNA.
- Base Composition, Computational Biology, Gene Transfer, Horizontal, Genomic Islands, Phylogeny.
Abstract
Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.
DOI: 10.1093/bioinformatics/btt727
PubMed: 24371153
Links to Exploration step
pubmed:24371153Le document en format XML
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<author><name sortKey="Jaron, Kamil S" sort="Jaron, Kamil S" uniqKey="Jaron K" first="Kamil S" last="Jaron">Kamil S. Jaron</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Moravec, Ji C" sort="Moravec, Ji C" uniqKey="Moravec J" first="Ji C" last="Moravec">Ji C. Moravec</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Martinkova, Natalia" sort="Martinkova, Natalia" uniqKey="Martinkova N" first="Natália" last="Martínková">Natália Martínková</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.</title>
<author><name sortKey="Jaron, Kamil S" sort="Jaron, Kamil S" uniqKey="Jaron K" first="Kamil S" last="Jaron">Kamil S. Jaron</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
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<author><name sortKey="Moravec, Ji C" sort="Moravec, Ji C" uniqKey="Moravec J" first="Ji C" last="Moravec">Ji C. Moravec</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
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<author><name sortKey="Martinkova, Natalia" sort="Martinkova, Natalia" uniqKey="Martinkova N" first="Natália" last="Martínková">Natália Martínková</name>
<affiliation><nlm:affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</nlm:affiliation>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
<imprint><date when="2014" type="published">2014</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Composition</term>
<term>Computational Biology</term>
<term>Eukaryota (genetics)</term>
<term>Gene Transfer, Horizontal</term>
<term>Genomic Islands</term>
<term>Genomics (methods)</term>
<term>Phylogeny</term>
<term>Sequence Analysis, DNA (methods)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Eukaryota</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Base Composition</term>
<term>Computational Biology</term>
<term>Gene Transfer, Horizontal</term>
<term>Genomic Islands</term>
<term>Phylogeny</term>
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<front><div type="abstract" xml:lang="en">Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.</div>
</front>
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<DateCompleted><Year>2017</Year>
<Month>11</Month>
<Day>02</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>30</Volume>
<Issue>8</Issue>
<PubDate><Year>2014</Year>
<Month>04</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.</ArticleTitle>
<Pagination><MedlinePgn>1081-1086</MedlinePgn>
</Pagination>
<Abstract><AbstractText Label="MOTIVATION">Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead.</AbstractText>
<AbstractText Label="RESULTS">We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition.</AbstractText>
<AbstractText Label="AVAILABILITY AND IMPLEMENTATION">Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research-data-analysis-tools-sighunt are implemented in C and R and are platform-independent.</AbstractText>
<AbstractText Label="CONTACT">376090@mail.muni.cz or martinkova@ivb.cz.</AbstractText>
<CopyrightInformation>© The Author 2013. 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>Jaron</LastName>
<ForeName>Kamil S</ForeName>
<Initials>KS</Initials>
<AffiliationInfo><Affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Moravec</LastName>
<ForeName>Jiří C</ForeName>
<Initials>JC</Initials>
<AffiliationInfo><Affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Martínková</LastName>
<ForeName>Natália</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic Institute of Biostatistics and Analyses, Masaryk University and Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.</Affiliation>
</AffiliationInfo>
</Author>
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<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
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<ArticleDate DateType="Electronic"><Year>2013</Year>
<Month>12</Month>
<Day>25</Day>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Bioinformatics</MedlineTA>
<NlmUniqueID>9808944</NlmUniqueID>
<ISSNLinking>1367-4803</ISSNLinking>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D001482" MajorTopicYN="N">Base Composition</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D056890" MajorTopicYN="N">Eukaryota</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D022761" MajorTopicYN="Y">Gene Transfer, Horizontal</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D044404" MajorTopicYN="Y">Genomic Islands</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
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<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName>
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<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
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<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year>
<Month>08</Month>
<Day>09</Day>
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<PubMedPubDate PubStatus="accepted"><Year>2013</Year>
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