Improved orthologous databases to ease protozoan targets inference

Detalhes bibliográficos
Autor(a) principal: Kotowski, Nelson
Data de Publicação: 2015
Outros Autores: Jardim, Rodrigo, Dávila, Alberto M. R.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/13544
Resumo: Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.
id CRUZ_af0bb2fb2b2338ebe3aa2d2857c01d09
oai_identifier_str oai:www.arca.fiocruz.br:icict/13544
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling Kotowski, NelsonJardim, RodrigoDávila, Alberto M. R.2016-04-05T17:52:09Z2016-04-05T17:52:09Z2015KOTOWSKI, Nelson; JARDIM, Rodrigo; DÁVILA, Alberto M. R. Improved orthologous databases to ease protozoan targets inference. Parasites & Vectors, v.8:494, 12p, 2015.1756-3305https://www.arca.fiocruz.br/handle/icict/1354410.1186/s13071-015-1090-0engBioMed CentralImproved orthologous databases to ease protozoan targets inferenceinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.Background: Homology inference helps on identifying similarities, as well as differences among organisms, which provides a better insight on how closely related one might be to another. In addition, comparative genomics pipelines are widely adopted tools designed using different bioinformatics applications and algorithms. In this article, we propose a methodology to build improved orthologous databases with the potential to aid on protozoan target identification, one of the many tasks which benefit from comparative genomics tools. Methods: Our analyses are based on OrthoSearch, a comparative genomics pipeline originally designed to infer orthologs through protein-profile comparison, supported by an HMM, reciprocal best hits based approach. Our methodology allows OrthoSearch to confront two orthologous databases and to generate an improved new one. Such can be later used to infer potential protozoan targets through a similarity analysis against the human genome. Results: The protein sequences of Cryptosporidium hominis, Entamoeba histolytica and Leishmania infantum genomes were comparatively analyzed against three orthologous databases: (i) EggNOG KOG, (ii) ProtozoaDB and (iii) Kegg Orthology (KO). That allowed us to create two new orthologous databases, “KO + EggNOG KOG” and “KO + EggNOG KOG + ProtozoaDB”, with 16,938 and 27,701 orthologous groups, respectively. Such new orthologous databases were used for a regular OrthoSearch run. By confronting “KO + EggNOG KOG” and “KO + EggNOG KOG + ProtozoaDB” databases and protozoan species we were able to detect the following total of orthologous groups and coverage (relation between the inferred orthologous groups and the species total number of proteins): Cryptosporidium hominis: 1,821 (11 %) and 3,254 (12 %); Entamoeba histolytica: 2,245 (13 %) and 5,305 (19 %); Leishmania infantum: 2,702 (16 %) and 4,760 (17 %). Using our HMM-based methodology and the largest created orthologous database, it was possible to infer 13 orthologous groups which represent potential protozoan targets; these were found because of our distant homology approach. We also provide the number of species-specific, pair-to-pair and core groups from such analyses, depicted in Venn diagrams. Conclusions: The orthologous databases generated by our HMM-based methodology provide a broader dataset, with larger amounts of orthologous groups when compared to the original databases used as input. Those may be used for several homology inference analyses, annotation tasks and protozoan targets identification.Comparative genomicsHomology inferenceTarget identificationProtozoaOrthologous databaseDistant homologyLeishmaniaCryptosporidiumEntamoebaEntamoebaLeishmaniaCryptosporidiumGenômicainfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/13544/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALalberto2_davila_etal_IOC_2015.pdfalberto2_davila_etal_IOC_2015.pdfapplication/pdf1760571https://www.arca.fiocruz.br/bitstream/icict/13544/2/alberto2_davila_etal_IOC_2015.pdfeb7dc1dfc939bbeb3f60a2e5dc9affdcMD52TEXTalberto2_davila_etal_IOC_2015.pdf.txtalberto2_davila_etal_IOC_2015.pdf.txtExtracted texttext/plain48866https://www.arca.fiocruz.br/bitstream/icict/13544/3/alberto2_davila_etal_IOC_2015.pdf.txt4dc16edb2677107f15581a2592fa4479MD53icict/135442023-09-05 10:26:02.322oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-05T13:26:02Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Improved orthologous databases to ease protozoan targets inference
title Improved orthologous databases to ease protozoan targets inference
spellingShingle Improved orthologous databases to ease protozoan targets inference
Kotowski, Nelson
Comparative genomics
Homology inference
Target identification
Protozoa
Orthologous database
Distant homology
Leishmania
Cryptosporidium
Entamoeba
Entamoeba
Leishmania
Cryptosporidium
Genômica
title_short Improved orthologous databases to ease protozoan targets inference
title_full Improved orthologous databases to ease protozoan targets inference
title_fullStr Improved orthologous databases to ease protozoan targets inference
title_full_unstemmed Improved orthologous databases to ease protozoan targets inference
title_sort Improved orthologous databases to ease protozoan targets inference
author Kotowski, Nelson
author_facet Kotowski, Nelson
Jardim, Rodrigo
Dávila, Alberto M. R.
author_role author
author2 Jardim, Rodrigo
Dávila, Alberto M. R.
author2_role author
author
dc.contributor.author.fl_str_mv Kotowski, Nelson
Jardim, Rodrigo
Dávila, Alberto M. R.
dc.subject.en.pt_BR.fl_str_mv Comparative genomics
Homology inference
Target identification
Protozoa
Orthologous database
Distant homology
Leishmania
Cryptosporidium
Entamoeba
topic Comparative genomics
Homology inference
Target identification
Protozoa
Orthologous database
Distant homology
Leishmania
Cryptosporidium
Entamoeba
Entamoeba
Leishmania
Cryptosporidium
Genômica
dc.subject.decs.pt_BR.fl_str_mv Entamoeba
Leishmania
Cryptosporidium
Genômica
description Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e Sistemas. Rio de Janeiro, RJ, Brasil.
publishDate 2015
dc.date.issued.fl_str_mv 2015
dc.date.accessioned.fl_str_mv 2016-04-05T17:52:09Z
dc.date.available.fl_str_mv 2016-04-05T17:52:09Z
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 KOTOWSKI, Nelson; JARDIM, Rodrigo; DÁVILA, Alberto M. R. Improved orthologous databases to ease protozoan targets inference. Parasites & Vectors, v.8:494, 12p, 2015.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/13544
dc.identifier.issn.none.fl_str_mv 1756-3305
dc.identifier.doi.none.fl_str_mv 10.1186/s13071-015-1090-0
identifier_str_mv KOTOWSKI, Nelson; JARDIM, Rodrigo; DÁVILA, Alberto M. R. Improved orthologous databases to ease protozoan targets inference. Parasites & Vectors, v.8:494, 12p, 2015.
1756-3305
10.1186/s13071-015-1090-0
url https://www.arca.fiocruz.br/handle/icict/13544
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 BioMed Central
publisher.none.fl_str_mv BioMed Central
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)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/13544/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/13544/2/alberto2_davila_etal_IOC_2015.pdf
https://www.arca.fiocruz.br/bitstream/icict/13544/3/alberto2_davila_etal_IOC_2015.pdf.txt
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
eb7dc1dfc939bbeb3f60a2e5dc9affdc
4dc16edb2677107f15581a2592fa4479
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1798324827092680704

Registros relacionados