Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands.
Identifieur interne : 000410 ( PubMed/Checkpoint ); précédent : 000409; suivant : 000411Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands.
Auteurs : Sangseon Lee ; Taeheon Lee ; Yung-Kyun Noh ; Sun KimSource :
- IEEE/ACM transactions on computational biology and bioinformatics [ 1557-9964 ] ; 2019.
Abstract
Existing k-mer based string kernel methods have been successfully used for sequence comparison. However, existing kernel methods have limitations for comparative and evolutionary comparisons of genomes due to the sensitiveness to over-represented k-mers and variable sequence lengths.
DOI: 10.1109/TCBB.2019.2938949
PubMed: 31494555
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands.</title><author><name sortKey="Lee, Sangseon" sort="Lee, Sangseon" uniqKey="Lee S" first="Sangseon" last="Lee">Sangseon Lee</name></author><author><name sortKey="Lee, Taeheon" sort="Lee, Taeheon" uniqKey="Lee T" first="Taeheon" last="Lee">Taeheon Lee</name></author><author><name sortKey="Noh, Yung Kyun" sort="Noh, Yung Kyun" uniqKey="Noh Y" first="Yung-Kyun" last="Noh">Yung-Kyun Noh</name></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31494555</idno><idno type="pmid">31494555</idno><idno type="doi">10.1109/TCBB.2019.2938949</idno><idno type="wicri:Area/PubMed/Corpus">000429</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000429</idno><idno type="wicri:Area/PubMed/Curation">000429</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000429</idno><idno type="wicri:Area/PubMed/Checkpoint">000410</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000410</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands.</title><author><name sortKey="Lee, Sangseon" sort="Lee, Sangseon" uniqKey="Lee S" first="Sangseon" last="Lee">Sangseon Lee</name></author><author><name sortKey="Lee, Taeheon" sort="Lee, Taeheon" uniqKey="Lee T" first="Taeheon" last="Lee">Taeheon Lee</name></author><author><name sortKey="Noh, Yung Kyun" sort="Noh, Yung Kyun" uniqKey="Noh Y" first="Yung-Kyun" last="Noh">Yung-Kyun Noh</name></author><author><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name></author></analytic><series><title level="j">IEEE/ACM transactions on computational biology and bioinformatics</title><idno type="eISSN">1557-9964</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Existing k-mer based string kernel methods have been successfully used for sequence comparison. However, existing kernel methods have limitations for comparative and evolutionary comparisons of genomes due to the sensitiveness to over-represented k-mers and variable sequence lengths.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">31494555</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1557-9964</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2019</Year><Month>Sep</Month><Day>03</Day></PubDate></JournalIssue><Title>IEEE/ACM transactions on computational biology and bioinformatics</Title><ISOAbbreviation>IEEE/ACM Trans Comput Biol Bioinform</ISOAbbreviation></Journal><ArticleTitle>Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1109/TCBB.2019.2938949</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Existing k-mer based string kernel methods have been successfully used for sequence comparison. However, existing kernel methods have limitations for comparative and evolutionary comparisons of genomes due to the sensitiveness to over-represented k-mers and variable sequence lengths.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this study, we propose a novel ranked k-spectrum string (RKSS) kernel. 1) RKSS kernel utilizes common k-mer sets across species, named landmarks, that can be used for comparing multiple genomes. 2) Based on the landmarks, we can use ranks of k-mers, rather than frequencies, that can produce more robust distances between genomes. To show the power of RKSS kernel, we conducted two experiments using 10 mammalian species with exon, intron, and CpG island sequences. RKSS kernel reconstructed more consistent evolutionary trees than the k-spectrum string kernel. In the subsequent experiment, for each sequence, kernel distance was calculated from 30 landmarks representing exon, intron, and CpG island sequences of 10 genomes. Based on kernel distances, concordance tests were performed and the result suggested that more information is conserved in CpG islands across species than in introns. In conclusion, our analysis suggests that the relational order, exon > CpG island > intron, in terms of evolutionary information contents.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Sangseon</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Taeheon</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Noh</LastName><ForeName>Yung-Kyun</ForeName><Initials>YK</Initials></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Sun</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>09</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>IEEE/ACM Trans Comput Biol Bioinform</MedlineTA><NlmUniqueID>101196755</NlmUniqueID><ISSNLinking>1545-5963</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>9</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>9</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>9</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31494555</ArticleId><ArticleId IdType="doi">10.1109/TCBB.2019.2938949</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Kim, Sun" sort="Kim, Sun" uniqKey="Kim S" first="Sun" last="Kim">Sun Kim</name><name sortKey="Lee, Sangseon" sort="Lee, Sangseon" uniqKey="Lee S" first="Sangseon" last="Lee">Sangseon Lee</name><name sortKey="Lee, Taeheon" sort="Lee, Taeheon" uniqKey="Lee T" first="Taeheon" last="Lee">Taeheon Lee</name><name sortKey="Noh, Yung Kyun" sort="Noh, Yung Kyun" uniqKey="Noh Y" first="Yung-Kyun" last="Noh">Yung-Kyun Noh</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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