WordCluster: detecting clusters of DNA words and genomic elements.
Identifieur interne : 001D25 ( PubMed/Checkpoint ); précédent : 001D24; suivant : 001D26WordCluster: detecting clusters of DNA words and genomic elements.
Auteurs : Michael Hackenberg [Espagne] ; Pedro Carpena ; Pedro Bernaola-Galván ; Guillermo Barturen ; Angel M. Alganza ; José L. OliverSource :
- Algorithms for molecular biology : AMB [ 1748-7188 ] ; 2011.
Abstract
Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.
DOI: 10.1186/1748-7188-6-2
PubMed: 21261981
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">WordCluster: detecting clusters of DNA words and genomic elements.</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:affiliation>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada, Spain. mlhack@gmail.com.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Angel M" last="Alganza">Angel M. Alganza</name></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21261981</idno><idno type="pmid">21261981</idno><idno type="doi">10.1186/1748-7188-6-2</idno><idno type="wicri:Area/PubMed/Corpus">001F09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F09</idno><idno type="wicri:Area/PubMed/Curation">001F09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F09</idno><idno type="wicri:Area/PubMed/Checkpoint">001D25</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001D25</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">WordCluster: detecting clusters of DNA words and genomic elements.</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:affiliation>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada, Spain. mlhack@gmail.com.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Angel M" last="Alganza">Angel M. Alganza</name></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></author></analytic><series><title level="j">Algorithms for molecular biology : AMB</title><idno type="eISSN">1748-7188</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">21261981</PMID><DateCompleted><Year>2011</Year><Month>07</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1748-7188</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><PubDate><Year>2011</Year><Month>Jan</Month><Day>24</Day></PubDate></JournalIssue><Title>Algorithms for molecular biology : AMB</Title><ISOAbbreviation>Algorithms Mol Biol</ISOAbbreviation></Journal><ArticleTitle>WordCluster: detecting clusters of DNA words and genomic elements.</ArticleTitle><Pagination><MedlinePgn>2</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1748-7188-6-2</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce here an algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used WordCluster to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">WordCluster seems to predict biological meaningful clusters of DNA words (k-mers) and genomic entities. The implementation of the method into a web server is available at http://bioinfo2.ugr.es/wordCluster/wordCluster.php including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hackenberg</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada, Spain. mlhack@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carpena</LastName><ForeName>Pedro</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Bernaola-Galván</LastName><ForeName>Pedro</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Barturen</LastName><ForeName>Guillermo</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Alganza</LastName><ForeName>Angel M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Oliver</LastName><ForeName>José L</ForeName><Initials>JL</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>01</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Algorithms Mol Biol</MedlineTA><NlmUniqueID>101265088</NlmUniqueID><ISSNLinking>1748-7188</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2010</Year><Month>08</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>01</Month><Day>24</Day></PubMedPubDate><PubMedPubDate 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sort="Alganza, Angel M" uniqKey="Alganza A" first="Angel M" last="Alganza">Angel M. Alganza</name><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></noCountry><country name="Espagne"><region name="Andalousie"><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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