TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes

Detalhes bibliográficos
Autor(a) principal: Oliveira, Mauro de Medeiros
Data de Publicação: 2021
Outros Autores: Bonadio, Igor, Melo, Alicia Lie de, Souza, Glaucia Mendes, Durham, Alan Mitchell
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/47751
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
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spelling Oliveira, Mauro de MedeirosBonadio, IgorMelo, Alicia Lie deSouza, Glaucia MendesDurham, Alan Mitchell2021-06-17T17:55:30Z2021-06-17T17:55:30Z2021OLIVEIRA, Mauro de Medeiros et al. TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. Briefings in Bioinformatics, p. 1–12, 2021.1477-4054https://www.arca.fiocruz.br/handle/icict/4775110.1093/bib/bbab198porOxford University PressTSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.Technology Company Elo7. São Paulo, SP, Brasil.Universidade de São Paulo. São Paulo, SP, Brasil.Universidade de São Paulo. Instituto de Química. São Paulo, SP, Brasil.Universidade de São Paulo. São Paulo, SP, Brasil.Promoter annotation is an important task in the analysis of a genome. One of the main challenges for this task is locating the border between the promoter region and the transcribing region of the gene, the transcription start site (TSS). The TSS is the reference point to delimit the DNA sequence responsible for the assembly of the transcribing complex. As the same gene can have more than one TSS, so to delimit the promoter region, it is important to locate the closest TSS to the site of the beginning of the translation. This paper presents TSSFinder, a new software for the prediction of the TSS signal of eukaryotic genes that is significantly more accurate than other available software.We currently are the only application to offer pre-trained models for six different eukaryotic organisms: Arabidopsis thaliana, Drosophila melanogaster, Gallus gallus, Homo sapiens, Oryza sativa and Saccharomyces cerevisiae. Additionally, our software can be easily customized for specific organisms using only 125 DNA sequences with a validated TSS signal and corresponding genomic locations as a training set. TSSFinder is a valuable new tool for the annotation of genomes. TSSFinder source code and docker container can be downloaded from http://tssfinder.github.io. Alternatively, TSSFinder is also available as a web service at http://sucest-fun.org/wsapp/tssfinder/.Transcription Initiation SitePromoter Regions, Geneticannotation of genomesGenomicsconditional random fieldsSitio de Iniciación de la TranscripciónRegiones Promotoras GenéticasGenómicaSite d'initiation de la transcriptionRégions promotrices (génétique)GénomiqueSítio de Iniciação de TranscriçãoRegiões Promotoras GenéticasGenômicainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-83084https://www.arca.fiocruz.br/bitstream/icict/47751/1/license.txt783568c2893d2e25a99990b126be1772MD51ORIGINALbbab19ok.pdfbbab19ok.pdfapplication/pdf523885https://www.arca.fiocruz.br/bitstream/icict/47751/2/bbab19ok.pdf6d00c547e455d9df4b4b4d622557ed14MD52TEXTbbab19ok.pdf.txtbbab19ok.pdf.txtExtracted 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dc.title.pt_BR.fl_str_mv TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
title TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
spellingShingle TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
Oliveira, Mauro de Medeiros
Transcription Initiation Site
Promoter Regions, Genetic
annotation of genomes
Genomics
conditional random fields
Sitio de Iniciación de la Transcripción
Regiones Promotoras Genéticas
Genómica
Site d'initiation de la transcription
Régions promotrices (génétique)
Génomique
Sítio de Iniciação de Transcrição
Regiões Promotoras Genéticas
Genômica
title_short TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
title_full TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
title_fullStr TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
title_full_unstemmed TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
title_sort TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes
author Oliveira, Mauro de Medeiros
author_facet Oliveira, Mauro de Medeiros
Bonadio, Igor
Melo, Alicia Lie de
Souza, Glaucia Mendes
Durham, Alan Mitchell
author_role author
author2 Bonadio, Igor
Melo, Alicia Lie de
Souza, Glaucia Mendes
Durham, Alan Mitchell
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Oliveira, Mauro de Medeiros
Bonadio, Igor
Melo, Alicia Lie de
Souza, Glaucia Mendes
Durham, Alan Mitchell
dc.subject.en.pt_BR.fl_str_mv Transcription Initiation Site
Promoter Regions, Genetic
annotation of genomes
Genomics
conditional random fields
topic Transcription Initiation Site
Promoter Regions, Genetic
annotation of genomes
Genomics
conditional random fields
Sitio de Iniciación de la Transcripción
Regiones Promotoras Genéticas
Genómica
Site d'initiation de la transcription
Régions promotrices (génétique)
Génomique
Sítio de Iniciação de Transcrição
Regiões Promotoras Genéticas
Genômica
dc.subject.es.pt_BR.fl_str_mv Sitio de Iniciación de la Transcripción
Regiones Promotoras Genéticas
Genómica
dc.subject.fr.pt_BR.fl_str_mv Site d'initiation de la transcription
Régions promotrices (génétique)
Génomique
dc.subject.decs.pt_BR.fl_str_mv Sítio de Iniciação de Transcrição
Regiões Promotoras Genéticas
Genômica
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Laboratório de Proteômica Estrutural e Computacional. Curitiba, PR, Brasil.
publishDate 2021
dc.date.accessioned.fl_str_mv 2021-06-17T17:55:30Z
dc.date.available.fl_str_mv 2021-06-17T17:55:30Z
dc.date.issued.fl_str_mv 2021
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.citation.fl_str_mv OLIVEIRA, Mauro de Medeiros et al. TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. Briefings in Bioinformatics, p. 1–12, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/47751
dc.identifier.issn.pt_BR.fl_str_mv 1477-4054
dc.identifier.doi.none.fl_str_mv 10.1093/bib/bbab198
identifier_str_mv OLIVEIRA, Mauro de Medeiros et al. TSSFinder—fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. Briefings in Bioinformatics, p. 1–12, 2021.
1477-4054
10.1093/bib/bbab198
url https://www.arca.fiocruz.br/handle/icict/47751
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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