ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences

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dc.contributor.authorFerro, Milene [UNESP]
dc.contributor.authorAntonio, Erik A.
dc.contributor.authorSouza, Wélliton [UNESP]
dc.contributor.authorBacci, Maurício [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionUniversidade Federal de São Carlos (UFSCar)
dc.date.accessioned2015-12-07T15:31:19Z
dc.date.available2015-12-07T15:31:19Z
dc.date.issued2014-11-27
dc.description.abstractStudies on fungal diversity and ecology aim to identify fungi and to investigate their interactions with each other and with the environment. DNA sequence-based tools are essential for these studies because they can speed up the identification process and access greater fungal diversity than traditional methods. The nucleotide sequence encoding for the internal transcribed spacer (ITS) of the nuclear ribosomal RNA has recently been proposed as a standard marker for molecular identification of fungi and evaluation of fungal diversity. However, the analysis of large sets of ITS sequences involves many programs and steps, which makes this task intensive and laborious. We developed the web-based pipeline ITScan, which automates the analysis of fungal ITS sequences generated either by Sanger or Next Generation Sequencing (NGS) platforms. Validation was performed using datasets containing ca. 2,000 to 40,000 sequences each. ITScan is an online and user-friendly automated pipeline for fungal diversity analysis and identification based on ITS sequences. It speeds up a process which would otherwise be repetitive and time-consuming for users. The ITScan tool and documentation are available at http://evol.rc.unesp.br:8083/itscan.en
dc.description.affiliationCentro de Estudos de Insetos Sociais (CEIS), Instituto de Biociências de Rio Claro (IBRC), Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brasil
dc.description.affiliationDepartamento de Bioquímica e Microbiologia, Instituto de Biociências de Rio Claro (IBRC), Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brasil
dc.description.affiliationDepartamento de Ciência da Computação, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, Brasil
dc.description.affiliationUnespUniversidade Estadual Paulista, Centro de Estudos de Insetos Sociais de Rio Claro
dc.description.affiliationUnespUniversidade Estadual Paulista, Departamento de Bioquímica e Microbiologia, Instituto de Biociências de Rio Claro
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipIdFAPESP: 2009/52289-9
dc.description.sponsorshipIdFAPESP: 2011/50226-0
dc.format.extent857-860
dc.identifierhttp://dx.doi.org/10.1186/1756-0500-7-857
dc.identifier.citationBMC Research Notes, v. 7, p. 857-860, 2014.
dc.identifier.doi10.1186/1756-0500-7-857
dc.identifier.filePMC4258023.pdf
dc.identifier.issn1756-0500
dc.identifier.pmcPMC4258023
dc.identifier.pubmed25430816
dc.identifier.urihttp://hdl.handle.net/11449/131067
dc.language.isoeng
dc.publisherBioMed Central
dc.relation.ispartofBMC Research Notes
dc.relation.ispartofsjr0,691
dc.rights.accessRightsAcesso aberto
dc.sourcePubMed
dc.subjectFungal biodiversityen
dc.subjectMycologyen
dc.subjectPipelineen
dc.subjectWeb serviceen
dc.titleITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequencesen
dc.typeArtigo
dcterms.rightsHolderBioMed Central LTD
unesp.author.orcid0000-0002-5619-1411[4]
unesp.campusUniversidade Estadual Paulista (Unesp), Instituto de Biociências, Rio Claropt

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Rio Claro - CEIS - Centro de Estudos de Insetos Sociais
Artigos - Bioquímica e Microbiologia - IBRC