SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.
Identifieur interne : 000065 ( PubMed/Corpus ); précédent : 000064; suivant : 000066SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.
Auteurs : Jee Eun Kang ; Antonio Ciampi ; Mohamed HijriSource :
- Genomics, proteomics & bioinformatics [ 2210-3244 ] ; 2020.
Abstract
In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important intra- and intermolecular interactions. SeSaMe PS Function is freely available for downloading at www.fungalsesame.org.
DOI: 10.1016/j.gpb.2018.07.011
PubMed: 33346085
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Electronic address: jekang_39@yahoo.com.</nlm:affiliation></affiliation></author><author><name sortKey="Ciampi, Antonio" sort="Ciampi, Antonio" uniqKey="Ciampi A" first="Antonio" last="Ciampi">Antonio Ciampi</name><affiliation><nlm:affiliation>Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Hijri, Mohamed" sort="Hijri, Mohamed" uniqKey="Hijri M" first="Mohamed" last="Hijri">Mohamed Hijri</name><affiliation><nlm:affiliation>Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, QC H1X 2B2, Canada; African Genome Center, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco. 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Electronic address: jekang_39@yahoo.com.</nlm:affiliation></affiliation></author><author><name sortKey="Ciampi, Antonio" sort="Ciampi, Antonio" uniqKey="Ciampi A" first="Antonio" last="Ciampi">Antonio Ciampi</name><affiliation><nlm:affiliation>Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Hijri, Mohamed" sort="Hijri, Mohamed" uniqKey="Hijri M" first="Mohamed" last="Hijri">Mohamed Hijri</name><affiliation><nlm:affiliation>Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, QC H1X 2B2, Canada; African Genome Center, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco. Electronic address: mohamed.hijri@umontreal.ca.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Genomics, proteomics & bioinformatics</title><idno type="eISSN">2210-3244</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important intra- and intermolecular interactions. SeSaMe PS Function is freely available for downloading at www.fungalsesame.org.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">33346085</PMID><DateRevised><Year>2021</Year><Month>06</Month><Day>15</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">2210-3244</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2020</Year><Month>Dec</Month><Day>18</Day></PubDate></JournalIssue><Title>Genomics, proteomics & bioinformatics</Title><ISOAbbreviation>Genomics Proteomics Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">S1672-0229(20)30139-X</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gpb.2018.07.011</ELocationID><Abstract><AbstractText>In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of 3-codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies 3-codon DNA 9-mers with structural roles, and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera. The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset. 3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important intra- and intermolecular interactions. SeSaMe PS Function is freely available for downloading at www.fungalsesame.org.</AbstractText><CopyrightInformation>Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Eun Kang</LastName><ForeName>Jee</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, QC H1X 2B2, Canada. Electronic address: jekang_39@yahoo.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ciampi</LastName><ForeName>Antonio</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC H3A 1A2, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hijri</LastName><ForeName>Mohamed</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, QC H1X 2B2, Canada; African Genome Center, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), 43150 Ben Guerir, Morocco. Electronic address: mohamed.hijri@umontreal.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>12</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Genomics Proteomics Bioinformatics</MedlineTA><NlmUniqueID>101197608</NlmUniqueID><ISSNLinking>1672-0229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Metagenome</Keyword><Keyword MajorTopicYN="N">Outlier</Keyword><Keyword MajorTopicYN="N">Position-specific function</Keyword><Keyword MajorTopicYN="N">SeSaMe</Keyword><Keyword MajorTopicYN="N">Spore-associated symbiotic microbes</Keyword></KeywordList><CoiStatement>Competing interests The authors have declared no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>10</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>07</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>07</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>12</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>12</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>12</Month><Day>21</Day><Hour>8</Hour><Minute>45</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33346085</ArticleId><ArticleId IdType="pii">S1672-0229(20)30139-X</ArticleId><ArticleId IdType="doi">10.1016/j.gpb.2018.07.011</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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