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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
25/04/2006 |
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Data da última atualização: |
17/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
HIGA, R. H.; CRUZ, S. A. B. da; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; FILETO, R.; MANCINI, A. L.; NESHICH, G. |
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Afiliação: |
ROBERTO HIROSHI HIGA, CNPTIA; SERGIO APARECIDO BRAGA DA CRUZ, CNPTIA; PAULA REGINA KUSER FALCAO, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA; RENATO FILETO, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; GORAN NESIC, CNPTIA. |
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Título: |
Building multiple sequence alignments with a flavour of HSSP alignments. |
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Ano de publicação: |
2005 |
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Fonte/Imprenta: |
In: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional, 2005. |
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Páginas: |
p. 28. |
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Idioma: |
Inglês |
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Notas: |
X-meeting 2005. Presented Posters. Na publicação: Paula Regina Kuser. |
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Conteúdo: |
HSSP is a well-know database of MSAs which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB databank. It is also used by STING and JavaProtein Dossier to calculate and present relative entropy as a measurement of a degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and JavaProtein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we have to have a new method for building alignments having a flavour of HSSP alignments (myMSAr). This work presents this new method and its corresponding databank (SH2Qs - database of Sequences Homologue to the Query [Structure-having] Sequence). Our main interest on making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless if it has a corresponding structure deposited in the PDB databank. In this work, we compare the measurement of residue conservation provided by corresponding alignments produced by the HSSP and SH2Qs. As a case study, we also present two biologically relevant examples, the former one highlighting the equivalence of analysis of a degree of residue conservation by using HSSP or SH2Qs alignments, and the later one presenting the degree of residue conservation for a structure modeled in a computer and, as a consequence, which does not have alignment reported by HSSP. MenosHSSP is a well-know database of MSAs which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB databank. It is also used by STING and JavaProtein Dossier to calculate and present relative entropy as a measurement of a degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and JavaProtein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we have to have a new method for building alignments having a flavour of HSSP alignments (myMSAr). This work presents this new method and its corresponding databank (SH2Qs - database of Sequences Homologue to the Query [Structure-having] Sequence). Our main interest on making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless if it has a corresponding structure deposited in the PDB databank. In this work, we compare the measurement of residue conservation provided by corresponding alignments produced by the HSSP and SH2Qs. As a case study, we also present two biologically relevant examples, the former one highlighting the equivalence of analysis of a degree of residue conservation by using HSSP or SH2Qs alignments, and the later one presenting the degree of residue conservation for a structure modeled in a computer and... Mostrar Tudo |
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Palavras-Chave: |
Entropia relativa; Multiple sequence alignment; Relative entropy; Residue conservation. |
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Thesagro: |
Proteina. |
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Thesaurus Nal: |
Sequence alignment. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02541nam a2200277 a 4500
001 1008967
005 2020-01-17
008 2005 bl uuuu u00u1 u #d
100 1 $aHIGA, R. H.
245 $aBuilding multiple sequence alignments with a flavour of HSSP alignments.$h[electronic resource]
260 $aIn: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional$c2005
300 $ap. 28.
500 $aX-meeting 2005. Presented Posters. Na publicação: Paula Regina Kuser.
520 $aHSSP is a well-know database of MSAs which merges information of protein sequences and their three-dimensional structures. It is available for all proteins whose structure is deposited in the PDB databank. It is also used by STING and JavaProtein Dossier to calculate and present relative entropy as a measurement of a degree of conservation for each residue of proteins whose structure has been solved and deposited in the PDB. However, if the STING and JavaProtein Dossier are to provide support for analysis of protein structures modeled in computers or being experimentally solved but not yet deposited in the PDB, then we have to have a new method for building alignments having a flavour of HSSP alignments (myMSAr). This work presents this new method and its corresponding databank (SH2Qs - database of Sequences Homologue to the Query [Structure-having] Sequence). Our main interest on making myMSAr was to measure the degree of residue conservation for a given query sequence, regardless if it has a corresponding structure deposited in the PDB databank. In this work, we compare the measurement of residue conservation provided by corresponding alignments produced by the HSSP and SH2Qs. As a case study, we also present two biologically relevant examples, the former one highlighting the equivalence of analysis of a degree of residue conservation by using HSSP or SH2Qs alignments, and the later one presenting the degree of residue conservation for a structure modeled in a computer and, as a consequence, which does not have alignment reported by HSSP.
650 $aSequence alignment
650 $aProteina
653 $aEntropia relativa
653 $aMultiple sequence alignment
653 $aRelative entropy
653 $aResidue conservation
700 1 $aCRUZ, S. A. B. da
700 1 $aFALCAO, P. R. K.
700 1 $aYAMAGISHI, M. E. B.
700 1 $aFILETO, R.
700 1 $aMANCINI, A. L.
700 1 $aNESHICH, G.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 5 | |
| 1. |  | PAPROTKA, T.; INOUE-NAGATA, A. K.; RESENDE, R.; JESKE, H.; RIBEIRO, S. G. Cloning and molecular analysis of sweet potato begomoviruses with Rolling circle amplication. Tropical Plant Pathology, Brasília, DF, v. 33, p. S292, ago. 2008. Suplemento. Resumo VIR 028. Trabalho apresentado no 41. Congresso Brasileiro de Fitopatologia, 41. Annual Meeting of the Brazilian Phytopathological Society, Belo Horizonte, 2008.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Hortaliças. |
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| 2. | | PAPROTKA, T.; INOURE NAGATA, A. K.; RESENDE, R.; JESKE, H.; RIBEIRO, S. G. Cloning and molecular analysis of sweet potato begomoviruses with rolling circle amplification. In: CONGRESSO BRASILEIRO DE FITOPATOLOGIA, 41., 2008, Belo Horizonte. [Resumos...]. Tropical Plant Pathology, v. 33, 2008. Suplemento. Resumo VIR-028. p. S291.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 3. | | PAPROTKA, T.; BOITEUX, L. S.; FONSECA, M. E. N.; RESENDE, R. O.; JESKE, H.; FARIA, J. C.; RIBEIRO, S. G. Genomic diversity of sweet potato geminiviruses in a Brazilian germplasm bank. Virus Research, Amsterdam, v. 149, n. 2, p. 224-233, May 2010.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Arroz e Feijão; Embrapa Hortaliças; Embrapa Recursos Genéticos e Biotecnologia. |
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| 4. | | PAPROTKA, T.; INOUE-NAGATA, A. K.; BOITEUX, L.; FONSECA, M. E. N.; RESENDE, R.; NAVAS-CASTILLO, J.; MORIONES, E.; JESKE, H.; FARIA, J. C.; RIBEIRO, S. G. Detecção, análise e clonagem de begomovirus de batata doce e feijão por amplificação por círculo rolante. In : ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 12., 2007, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2007. p. 66.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 5. | | PAPROTKA, T.; INOUE-NAGATA, A. K.; BOITEUX, L.; FONSECA, M. E. N.; RESENDE, R.; NAVAS-CASTILLO, J.; MORIONES, E.; JESKE, H.; FARIA, J. C.; RIBEIRO, S. G. Detecção, análise e clonagem de begomovirus de batata doce e feijão por amplificação por círculo rolante. In: ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 12., 2007, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2007. p. 67.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Arroz e Feijão. |
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| Registros recuperados : 5 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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