A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters

Detalhes bibliográficos
Autor(a) principal: Kroll, José Eduardo
Data de Publicação: 2017
Outros Autores: Silva, Vandeclecio Lira da, Souza, Sandro José de, Souza, Gustavo Antonio de
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFRN
Texto Completo: https://repositorio.ufrn.br/jspui/handle/123456789/23831
Resumo: 2020-12
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spelling Kroll, José EduardoSilva, Vandeclecio Lira daSouza, Sandro José deSouza, Gustavo Antonio de2017-09-11T17:08:26Z2017-07https://repositorio.ufrn.br/jspui/handle/123456789/2383110.1002/bies.201700015engWileyalternative splicing eventsgenome browsermass spectrometrypeptide identificationproteogenomicsA tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parametersinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2020-12In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry-based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non-coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRNinstname:Universidade Federal do Rio Grande do Norte (UFRN)instacron:UFRNLICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://repositorio.ufrn.br/bitstream/123456789/23831/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52TEXTSandroSouza_ICe_2017_A tool for integrating.pdf.txtSandroSouza_ICe_2017_A tool for integrating.pdf.txtExtracted texttext/plain51551https://repositorio.ufrn.br/bitstream/123456789/23831/5/SandroSouza_ICe_2017_A%20tool%20for%20integrating.pdf.txt75f14a534733c01f0b34803472c1ee63MD55THUMBNAILSandroSouza_ICe_2017_A tool for integrating.pdf.jpgSandroSouza_ICe_2017_A tool for integrating.pdf.jpgIM Thumbnailimage/jpeg9898https://repositorio.ufrn.br/bitstream/123456789/23831/6/SandroSouza_ICe_2017_A%20tool%20for%20integrating.pdf.jpga7430863340274e4576a143709ae3c8bMD56123456789/238312024-03-19 01:02:32.704oai:https://repositorio.ufrn.br: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Repositório de PublicaçõesPUBhttp://repositorio.ufrn.br/oai/opendoar:2024-03-19T04:02:32Repositório Institucional da UFRN - Universidade Federal do Rio Grande do Norte (UFRN)false
dc.title.pt_BR.fl_str_mv A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
title A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
spellingShingle A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
Kroll, José Eduardo
alternative splicing events
genome browser
mass spectrometry
peptide identification
proteogenomics
title_short A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
title_full A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
title_fullStr A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
title_full_unstemmed A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
title_sort A tool for integrating genetic and mass spectrometry-based peptide data: proteogenomics viewer: PV: a genome browser-like tool, which includes MS data visualization and peptide identification parameters
author Kroll, José Eduardo
author_facet Kroll, José Eduardo
Silva, Vandeclecio Lira da
Souza, Sandro José de
Souza, Gustavo Antonio de
author_role author
author2 Silva, Vandeclecio Lira da
Souza, Sandro José de
Souza, Gustavo Antonio de
author2_role author
author
author
dc.contributor.author.fl_str_mv Kroll, José Eduardo
Silva, Vandeclecio Lira da
Souza, Sandro José de
Souza, Gustavo Antonio de
dc.subject.por.fl_str_mv alternative splicing events
genome browser
mass spectrometry
peptide identification
proteogenomics
topic alternative splicing events
genome browser
mass spectrometry
peptide identification
proteogenomics
description 2020-12
publishDate 2017
dc.date.accessioned.fl_str_mv 2017-09-11T17:08:26Z
dc.date.issued.fl_str_mv 2017-07
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 https://repositorio.ufrn.br/jspui/handle/123456789/23831
dc.identifier.doi.none.fl_str_mv 10.1002/bies.201700015
url https://repositorio.ufrn.br/jspui/handle/123456789/23831
identifier_str_mv 10.1002/bies.201700015
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Wiley
publisher.none.fl_str_mv Wiley
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFRN
instname:Universidade Federal do Rio Grande do Norte (UFRN)
instacron:UFRN
instname_str Universidade Federal do Rio Grande do Norte (UFRN)
instacron_str UFRN
institution UFRN
reponame_str Repositório Institucional da UFRN
collection Repositório Institucional da UFRN
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