SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.
Identifieur interne : 000759 ( Main/Exploration ); précédent : 000758; suivant : 000760SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.
Auteurs : Jee Eun Kang [Canada] ; Antonio Ciampi [Canada] ; Mohamed Hijri [Maroc]Source :
- 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
Affiliations:
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Electronic address: mohamed.hijri@umontreal.ca.</nlm:affiliation><country xml:lang="fr">Maroc</country><wicri:regionArea>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</wicri:regionArea><wicri:noRegion>43150 Ben Guerir</wicri:noRegion></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. 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