K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.
Identifieur interne : 000C51 ( PubMed/Checkpoint ); précédent : 000C50; suivant : 000C52K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.
Auteurs : Aaron Sievers [Allemagne] ; Katharina Bosiek [Allemagne] ; Marc Bisch [Allemagne] ; Chris Dreessen [Allemagne] ; Jascha Riedel [Allemagne] ; Patrick Fro [Allemagne] ; Michael Hausmann [Allemagne] ; Georg Hildenbrand [Allemagne]Source :
- Genes [ 2073-4425 ] ; 2017.
Abstract
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard k-mer analysis.
DOI: 10.3390/genes8040122
PubMed: 28422050
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Sievers_Aaron@web.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Bosiek, Katharina" sort="Bosiek, Katharina" uniqKey="Bosiek K" first="Katharina" last="Bosiek">Katharina Bosiek</name><affiliation wicri:level="3"><nlm:affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. 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Fross@stud.uni-heidelberg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Hausmann, Michael" sort="Hausmann, Michael" uniqKey="Hausmann M" first="Michael" last="Hausmann">Michael Hausmann</name><affiliation wicri:level="3"><nlm:affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. hausmann@kip.uni-heidelberg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Hildenbrand, Georg" sort="Hildenbrand, Georg" uniqKey="Hildenbrand G" first="Georg" last="Hildenbrand">Georg Hildenbrand</name><affiliation wicri:level="3"><nlm:affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. hilden@kip.uni-heidelberg.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author></analytic><series><title level="j">Genes</title><idno type="ISSN">2073-4425</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In genome analysis, <i>k-mer</i>-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve <i>k</i>-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local <i>k</i>-mer spectra (frequency distribution of <i>k</i>-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ <i>k</i> ≤ 4) on relatively small viral genomes of <i>Papillomaviridae</i> and <i>Herpesviridae</i>, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in <i>Papillomaviridae</i> and <i>Herpesviridae</i> formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the <i>k</i>-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown <i>k</i>-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest <i>k</i>-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard <i>k</i>-mer analysis.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28422050</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2073-4425</ISSN><JournalIssue CitedMedium="Print"><Volume>8</Volume><Issue>4</Issue><PubDate><Year>2017</Year><Month>Apr</Month><Day>19</Day></PubDate></JournalIssue><Title>Genes</Title><ISOAbbreviation>Genes (Basel)</ISOAbbreviation></Journal><ArticleTitle>K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E122</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/genes8040122</ELocationID><Abstract><AbstractText>In genome analysis, <i>k-mer</i>-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve <i>k</i>-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local <i>k</i>-mer spectra (frequency distribution of <i>k</i>-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ <i>k</i> ≤ 4) on relatively small viral genomes of <i>Papillomaviridae</i> and <i>Herpesviridae</i>, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in <i>Papillomaviridae</i> and <i>Herpesviridae</i> formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the <i>k</i>-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown <i>k</i>-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest <i>k</i>-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of standard <i>k</i>-mer analysis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sievers</LastName><ForeName>Aaron</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. Sievers_Aaron@web.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bosiek</LastName><ForeName>Katharina</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. KatharinaBosiek@gmx.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bisch</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. MarcBisch@gmx.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dreessen</LastName><ForeName>Chris</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. chrisdreessen@yahoo.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Riedel</LastName><ForeName>Jascha</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. jaschelite@googlemail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Froß</LastName><ForeName>Patrick</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. Fross@stud.uni-heidelberg.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hausmann</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. hausmann@kip.uni-heidelberg.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hildenbrand</LastName><ForeName>Georg</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Kirchhoff-Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany. hilden@kip.uni-heidelberg.de.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany. hilden@kip.uni-heidelberg.de.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Genes (Basel)</MedlineTA><NlmUniqueID>101551097</NlmUniqueID><ISSNLinking>2073-4425</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">alignment-free</Keyword><Keyword MajorTopicYN="N">k-mer</Keyword><Keyword MajorTopicYN="N">k-mer analysis</Keyword><Keyword MajorTopicYN="N">positional features</Keyword><Keyword MajorTopicYN="N">sequence analysis</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>02</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>03</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>04</Day></PubMedPubDate><PubMedPubDate 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last="Bosiek">Katharina Bosiek</name><name sortKey="Dreessen, Chris" sort="Dreessen, Chris" uniqKey="Dreessen C" first="Chris" last="Dreessen">Chris Dreessen</name><name sortKey="Fro, Patrick" sort="Fro, Patrick" uniqKey="Fro P" first="Patrick" last="Fro">Patrick Fro</name><name sortKey="Hausmann, Michael" sort="Hausmann, Michael" uniqKey="Hausmann M" first="Michael" last="Hausmann">Michael Hausmann</name><name sortKey="Hildenbrand, Georg" sort="Hildenbrand, Georg" uniqKey="Hildenbrand G" first="Georg" last="Hildenbrand">Georg Hildenbrand</name><name sortKey="Riedel, Jascha" sort="Riedel, Jascha" uniqKey="Riedel J" first="Jascha" last="Riedel">Jascha Riedel</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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