A Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja

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Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUTFPR-
Autor(es): dc.contributorUniversidade Estadual de Londrina (UEL)-
Autor(es): dc.creatorDomingues, Douglas S.-
Autor(es): dc.creatorOliveira, Liliane S.-
Autor(es): dc.creatorLemos, Samara M. C.-
Autor(es): dc.creatorBarros, Gian C. C.-
Autor(es): dc.creatorIvamoto-Suzuki, Suzana T.-
Data de aceite: dc.date.accessioned2025-08-21T17:20:04Z-
Data de disponibilização: dc.date.available2025-08-21T17:20:04Z-
Data de envio: dc.date.issued2023-03-01-
Data de envio: dc.date.issued2023-03-01-
Data de envio: dc.date.issued2021-12-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1007/978-1-0716-2185-1_4-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/239995-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/239995-
Descrição: dc.descriptionTerpenoids are a class of compounds that are found in all living organisms. In plants, some terpenoids are part of primary metabolism, but most terpenes found in plants are classified as specialized metabolites, encoded by terpene synthases (TPS). It is not obvious how to assign the putative product of a given TPS using bioinformatics tools. Phylogenetic analyses easily assign TPS into families; however members of the same TPS family can synthetize more than one terpenoid—and, in many biotechnological applications, researchers are more interested in the product of a given TPS rather than its phylogenetic profile. Automated protein annotation can be used to classify TPS based on their products, despite the family they belong to. Here, we implement an automated bioinformatics method, search_TPS, to identify TPS proteins that synthesize mono, sesqui and diterpenes in Angiosperms. We verified the applicability of the method by classifying wet lab validated TPS and applying it to find TPS proteins in Coffea arabica, C. canephora, C. eugenioides, and Quillaja saponaria. Search_TPS is a computational tool based on PERL scripts that carries out a series of HMMER searches against a curated database of TPS profile hidden Markov models. The tool is freely available at https://github.com/liliane-sntn/TPS.-
Descrição: dc.descriptionGroup of Genomics and Transcriptomes in Plants Institute of Biosciences São Paulo State University UNESP-
Descrição: dc.descriptionGraduate Program in Bioinformatics Federal University of Technology - Paraná UTFPR-
Descrição: dc.descriptionGraduate Program in Genetics Institute of Biosciences São Paulo State University UNESP-
Descrição: dc.descriptionGraduate Program in Plant Biology Institute of Biosciences São Paulo State University UNESP-
Descrição: dc.descriptionDepartment of Agronomy State University of Londrina UEL-
Descrição: dc.descriptionGroup of Genomics and Transcriptomes in Plants Institute of Biosciences São Paulo State University UNESP-
Descrição: dc.descriptionGraduate Program in Genetics Institute of Biosciences São Paulo State University UNESP-
Descrição: dc.descriptionGraduate Program in Plant Biology Institute of Biosciences São Paulo State University UNESP-
Formato: dc.format43-53-
Idioma: dc.languageen-
Relação: dc.relationMethods in Molecular Biology-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectDiterpene-
Palavras-chave: dc.subjectMonoterpene-
Palavras-chave: dc.subjectProfile HMMs-
Palavras-chave: dc.subjectSesquiterpene-
Palavras-chave: dc.subjectTerpene synthase-
Título: dc.titleA Bioinformatics Tool for Efficient Retrieval of High-Confidence Terpene Synthases (TPS) and Application to the Identification of TPS in Coffea and Quillaja-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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