Genomic classification using an information-based similarity index: application to the SARS coronavirus.
Identifieur interne : 004B14 ( Main/Merge ); précédent : 004B13; suivant : 004B15Genomic classification using an information-based similarity index: application to the SARS coronavirus.
Auteurs : Albert C-C Yang [États-Unis] ; Ary L. Goldberger ; C-K PengSource :
- Journal of computational biology : a journal of computational molecular cell biology [ 1066-5277 ] ; 2005.
Descripteurs français
- KwdFr :
- ADN mitochondrial, Alignement de séquences, Analyse de regroupements, Analyse de séquence d'ADN (), Bases de données d'acides nucléiques, Données de séquences moléculaires, Humains, Phylogénie, Séquence nucléotidique, Virus de la grippe A (génétique), Virus du SRAS (), Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- génétique : Virus de la grippe A, Virus du SRAS.
- ADN mitochondrial, Alignement de séquences, Analyse de regroupements, Analyse de séquence d'ADN, Bases de données d'acides nucléiques, Données de séquences moléculaires, Humains, Phylogénie, Séquence nucléotidique, Virus du SRAS, Évolution moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA, Mitochondrial.
- classification : SARS Virus.
- genetics : Influenza A virus, SARS Virus.
- methods : Sequence Analysis, DNA.
- Base Sequence, Cluster Analysis, Databases, Nucleic Acid, Evolution, Molecular, Humans, Molecular Sequence Data, Phylogeny, Sequence Alignment.
Abstract
Measures of genetic distance based on alignment methods are confined to studying sequences that are conserved and identifiable in all organisms under study. A number of alignment-free techniques based on either statistical linguistics or information theory have been developed to overcome the limitations of alignment methods. We present a novel alignment-free approach to measuring the similarity among genetic sequences that incorporates elements from both word rank order-frequency statistics and information theory. We first validate this method on the human influenza A viral genomes as well as on the human mitochondrial DNA database. We then apply the method to study the origin of the SARS coronavirus. We find that the majority of the SARS genome is most closely related to group 1 coronaviruses, with smaller regions of matches to sequences from groups 2 and 3. The information based similarity index provides a new tool to measure the similarity between datasets based on their information content and may have a wide range of applications in the large-scale analysis of genomic databases.
DOI: 10.1089/cmb.2005.12.1103
PubMed: 16241900
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pubmed:16241900Le document en format XML
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Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts 02215</wicri:regionArea><wicri:noRegion>Massachusetts 02215</wicri:noRegion></affiliation></author><author><name sortKey="Goldberger, Ary L" sort="Goldberger, Ary L" uniqKey="Goldberger A" first="Ary L" last="Goldberger">Ary L. Goldberger</name></author><author><name sortKey="Peng, C K" sort="Peng, C K" uniqKey="Peng C" first="C-K" last="Peng">C-K Peng</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2005">2005</date><idno type="RBID">pubmed:16241900</idno><idno type="pmid">16241900</idno><idno type="doi">10.1089/cmb.2005.12.1103</idno><idno type="wicri:Area/PubMed/Corpus">002486</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002486</idno><idno type="wicri:Area/PubMed/Curation">002486</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002486</idno><idno type="wicri:Area/PubMed/Checkpoint">002695</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002695</idno><idno type="wicri:Area/Ncbi/Merge">001220</idno><idno type="wicri:Area/Ncbi/Curation">001220</idno><idno type="wicri:Area/Ncbi/Checkpoint">001220</idno><idno type="wicri:doubleKey">1066-5277:2005:Yang A:genomic:classification:using</idno><idno type="wicri:Area/Main/Merge">004B14</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomic classification using an information-based similarity index: application to the SARS coronavirus.</title><author><name sortKey="Yang, Albert C C" sort="Yang, Albert C C" uniqKey="Yang A" first="Albert C-C" last="Yang">Albert C-C Yang</name><affiliation wicri:level="1"><nlm:affiliation>Cardiovascular Division and Margret and H.A. Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts 02215, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cardiovascular Division and Margret and H.A. Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts 02215</wicri:regionArea><wicri:noRegion>Massachusetts 02215</wicri:noRegion></affiliation></author><author><name sortKey="Goldberger, Ary L" sort="Goldberger, Ary L" uniqKey="Goldberger A" first="Ary L" last="Goldberger">Ary L. Goldberger</name></author><author><name sortKey="Peng, C K" sort="Peng, C K" uniqKey="Peng C" first="C-K" last="Peng">C-K Peng</name></author></analytic><series><title level="j">Journal of computational biology : a journal of computational molecular cell biology</title><idno type="ISSN">1066-5277</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Cluster Analysis</term><term>DNA, Mitochondrial</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Humans</term><term>Influenza A virus (genetics)</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN mitochondrial</term><term>Alignement de séquences</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN ()</term><term>Bases de données d'acides nucléiques</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Phylogénie</term><term>Séquence nucléotidique</term><term>Virus de la grippe A (génétique)</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A virus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus de la grippe A</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Cluster Analysis</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN mitochondrial</term><term>Alignement de séquences</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Bases de données d'acides nucléiques</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Phylogénie</term><term>Séquence nucléotidique</term><term>Virus du SRAS</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Measures of genetic distance based on alignment methods are confined to studying sequences that are conserved and identifiable in all organisms under study. A number of alignment-free techniques based on either statistical linguistics or information theory have been developed to overcome the limitations of alignment methods. We present a novel alignment-free approach to measuring the similarity among genetic sequences that incorporates elements from both word rank order-frequency statistics and information theory. We first validate this method on the human influenza A viral genomes as well as on the human mitochondrial DNA database. We then apply the method to study the origin of the SARS coronavirus. We find that the majority of the SARS genome is most closely related to group 1 coronaviruses, with smaller regions of matches to sequences from groups 2 and 3. The information based similarity index provides a new tool to measure the similarity between datasets based on their information content and may have a wide range of applications in the large-scale analysis of genomic databases.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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