ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/1756-0500-7-857 http://hdl.handle.net/11449/131067 |
Resumo: | Studies 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. |
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ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequencesFungal biodiversityMycologyPipelineWeb serviceStudies 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.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Centro de Estudos de Insetos Sociais (CEIS), Instituto de Biociências de Rio Claro (IBRC), Universidade Estadual Paulista (UNESP), Rio Claro, SP, BrasilDepartamento de Bioquímica e Microbiologia, Instituto de Biociências de Rio Claro (IBRC), Universidade Estadual Paulista (UNESP), Rio Claro, SP, BrasilDepartamento de Ciência da Computação, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, BrasilUniversidade Estadual Paulista, Centro de Estudos de Insetos Sociais de Rio ClaroUniversidade Estadual Paulista, Departamento de Bioquímica e Microbiologia, Instituto de Biociências de Rio ClaroFAPESP: 2009/52289-9FAPESP: 2011/50226-0BioMed CentralUniversidade Estadual Paulista (Unesp)Universidade Federal de São Carlos (UFSCar)Ferro, Milene [UNESP]Antonio, Erik A.Souza, Wélliton [UNESP]Bacci, Maurício [UNESP]2015-12-07T15:31:19Z2015-12-07T15:31:19Z2014-11-27info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article857-860application/pdfhttp://dx.doi.org/10.1186/1756-0500-7-857BMC Research Notes, v. 7, p. 857-860, 2014.1756-0500http://hdl.handle.net/11449/13106710.1186/1756-0500-7-857PMC4258023.pdf25430816PMC4258023PubMedreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Research Notes0,691info:eu-repo/semantics/openAccess2024-04-11T14:57:10Zoai:repositorio.unesp.br:11449/131067Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:32:02.786233Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
title |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
spellingShingle |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences Ferro, Milene [UNESP] Fungal biodiversity Mycology Pipeline Web service |
title_short |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
title_full |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
title_fullStr |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
title_full_unstemmed |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
title_sort |
ITScan: a web-based analysis tool for Internal Transcribed Spacer (ITS) sequences |
author |
Ferro, Milene [UNESP] |
author_facet |
Ferro, Milene [UNESP] Antonio, Erik A. Souza, Wélliton [UNESP] Bacci, Maurício [UNESP] |
author_role |
author |
author2 |
Antonio, Erik A. Souza, Wélliton [UNESP] Bacci, Maurício [UNESP] |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade Federal de São Carlos (UFSCar) |
dc.contributor.author.fl_str_mv |
Ferro, Milene [UNESP] Antonio, Erik A. Souza, Wélliton [UNESP] Bacci, Maurício [UNESP] |
dc.subject.por.fl_str_mv |
Fungal biodiversity Mycology Pipeline Web service |
topic |
Fungal biodiversity Mycology Pipeline Web service |
description |
Studies 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. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-11-27 2015-12-07T15:31:19Z 2015-12-07T15:31:19Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/1756-0500-7-857 BMC Research Notes, v. 7, p. 857-860, 2014. 1756-0500 http://hdl.handle.net/11449/131067 10.1186/1756-0500-7-857 PMC4258023.pdf 25430816 PMC4258023 |
url |
http://dx.doi.org/10.1186/1756-0500-7-857 http://hdl.handle.net/11449/131067 |
identifier_str_mv |
BMC Research Notes, v. 7, p. 857-860, 2014. 1756-0500 10.1186/1756-0500-7-857 PMC4258023.pdf 25430816 PMC4258023 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
BMC Research Notes 0,691 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
857-860 application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
dc.source.none.fl_str_mv |
PubMed reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128668310962176 |