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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
02/12/2010 |
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Data da última atualização: |
27/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
HERAI, R. H.; YAMAGISHI, M. E. B. |
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Afiliação: |
ROBERTO H. HERAI, IB/UNICAMP; MICHEL E. B. YAMAGISHI, CNPTIA. |
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Título: |
A bioinformatics approach to detect interchromosomal trans-splicing in bovine full length cDNA databanks. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
In: PLANT & ANIMAL GENOME CONFERENCE, 18., 2010, San Diego. Abstracts... [S.l.: s.n.], 2010. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês |
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Notas: |
P869. PAG-XVIII. |
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Conteúdo: |
Trans-splicing is an unusual form of RNA processing mechanism where distinct pre-mRNA sequences contribute to the formation of a single mRNA. It is common in nematodes and kinetoplastids, but it is rare in superior organisms. Nevertheless, some recent studies show that trans-splicing, although rare, may be more widespread than believed (Gingeras). Consequently, its identification in large databanks is very important for posteriori experimental confirmation. Recently, we have developed a Bioinformatic methodology that successfully found 16 inter-chromosomal trans-splicing candidate sequences in a large human full length cDNA (FlcDNA) databank (Herai & Yamagishi, in press). Unfortunately, our methodology was supposed to be applied on organisms with high quality reference genome, otherwise the number of false positive candidate sequences turned the analysis prohibitive. The problem is that many important model organisms have only draft assemblies. In order to overcome this problem, we extended our bioinformatics methodology applying additional filtering criteria and ad hoc algorithms necessary to deal with those cases. Using 83,048 bovine FlcDNA transcripts (NCBI, MGC, BGD) and Bos taurus UMD 3.0 genome assembly, our extended methodology successfully found 12 hybrid mRNAs which may be the first instances of bovine inter-chromosomal trans-splicing sequences, since the single reported bovine trans-splicing evidence was an intra-chromosomal instance (Roux et al.). Furthermore, just like in the human case, the bovine candidate sequence gene loci had many inverted repeat sequences which may support the conjecture that those sequences may be part of a non-spliceosome mediated trans-splicing mechanism (Di Segni et al.). MenosTrans-splicing is an unusual form of RNA processing mechanism where distinct pre-mRNA sequences contribute to the formation of a single mRNA. It is common in nematodes and kinetoplastids, but it is rare in superior organisms. Nevertheless, some recent studies show that trans-splicing, although rare, may be more widespread than believed (Gingeras). Consequently, its identification in large databanks is very important for posteriori experimental confirmation. Recently, we have developed a Bioinformatic methodology that successfully found 16 inter-chromosomal trans-splicing candidate sequences in a large human full length cDNA (FlcDNA) databank (Herai & Yamagishi, in press). Unfortunately, our methodology was supposed to be applied on organisms with high quality reference genome, otherwise the number of false positive candidate sequences turned the analysis prohibitive. The problem is that many important model organisms have only draft assemblies. In order to overcome this problem, we extended our bioinformatics methodology applying additional filtering criteria and ad hoc algorithms necessary to deal with those cases. Using 83,048 bovine FlcDNA transcripts (NCBI, MGC, BGD) and Bos taurus UMD 3.0 genome assembly, our extended methodology successfully found 12 hybrid mRNAs which may be the first instances of bovine inter-chromosomal trans-splicing sequences, since the single reported bovine trans-splicing evidence was an intra-chromosomal instance (Roux et al.). Furthermore, jus... Mostrar Tudo |
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Palavras-Chave: |
Algoritmo; Bioinformática. |
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Thesaurus Nal: |
Algorithms; Bioinformatics; RNA splicing. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/91866/1/869.pdf
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Marc: |
LEADER 02405nam a2200205 a 4500
001 1868482
005 2020-01-27
008 2010 bl uuuu u01u1 u #d
100 1 $aHERAI, R. H.
245 $aA bioinformatics approach to detect interchromosomal trans-splicing in bovine full length cDNA databanks.$h[electronic resource]
260 $aIn: PLANT & ANIMAL GENOME CONFERENCE, 18., 2010, San Diego. Abstracts... [S.l.: s.n.]$c2010
300 $aNão paginado.
500 $aP869. PAG-XVIII.
520 $aTrans-splicing is an unusual form of RNA processing mechanism where distinct pre-mRNA sequences contribute to the formation of a single mRNA. It is common in nematodes and kinetoplastids, but it is rare in superior organisms. Nevertheless, some recent studies show that trans-splicing, although rare, may be more widespread than believed (Gingeras). Consequently, its identification in large databanks is very important for posteriori experimental confirmation. Recently, we have developed a Bioinformatic methodology that successfully found 16 inter-chromosomal trans-splicing candidate sequences in a large human full length cDNA (FlcDNA) databank (Herai & Yamagishi, in press). Unfortunately, our methodology was supposed to be applied on organisms with high quality reference genome, otherwise the number of false positive candidate sequences turned the analysis prohibitive. The problem is that many important model organisms have only draft assemblies. In order to overcome this problem, we extended our bioinformatics methodology applying additional filtering criteria and ad hoc algorithms necessary to deal with those cases. Using 83,048 bovine FlcDNA transcripts (NCBI, MGC, BGD) and Bos taurus UMD 3.0 genome assembly, our extended methodology successfully found 12 hybrid mRNAs which may be the first instances of bovine inter-chromosomal trans-splicing sequences, since the single reported bovine trans-splicing evidence was an intra-chromosomal instance (Roux et al.). Furthermore, just like in the human case, the bovine candidate sequence gene loci had many inverted repeat sequences which may support the conjecture that those sequences may be part of a non-spliceosome mediated trans-splicing mechanism (Di Segni et al.).
650 $aAlgorithms
650 $aBioinformatics
650 $aRNA splicing
653 $aAlgoritmo
653 $aBioinformática
700 1 $aYAMAGISHI, M. E. B.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 233 | |
| 2. |  | NARCISO, M. G.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R.; NESHICH, G. 2D maps of protein surface. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster B-63.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 4. | | YAMAGISHI, M. E. B.; MARTINS, N. F.; NESHICH, G.; CAI, W.; SHAO, X.; BEAUTRAIT, A.; MAIGRET, B. A fast surface-matching procedure for protein-ligand docking. Journal of Molecular Modeling, v. 12, n. 6, p. 965-972, Sept. 2006.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: -- - A |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 9. | | QUEIROS, L. R.; VISOLI, M. C.; YAMAGISHI, M. E. B.; IDE, F. H.; VACARI, I.; SANTOS, A. D. dos; COSTA, I. R. S.; BENITO, N. P. Alelo - Gestor Integrado de Recursos Genéticos - Processo Análise Quarentenária de Germoplasma Vegetal (planejamento, acompanhamento e finalização). Versão 0.32. Campinas: Embrapa Informática Agropecuária, 2012. 1 CD-ROM.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | IDE, F. H.; VISOLI, M. C.; YAMAGISHI, M. E. B.; VACARI, I.; SANTOS, A. D. dos; QUEIROS, L. R.; COSTAS, I. R. S.; JOSÉ, S. C. B. R.; PÁDUA, J. G. Alelo - Gestor Integrado de Recursos Genéticos - Processo de Atendimento de Solicitação de Germoplasma Semente da coleção Colbase. Versão 0.32. Campinas: Embrapa Informática Agropecuária, 2012. 1 CD-ROM.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 11. | | IDE, F. H.; VISOLI, M. C.; YAMAGISHI, M. E. B.; VACARI, I.; SANTOS, A. D. dos; QUEIROS, L. R.; COSTA, I. R. S.; JOSE, S. C. B. R.; PÁDUA, J. G. Alelo - Gestor Integrado de Recursos Genéticos - Processo de Incorporação de Germoplasma Semente à coleção Colbase. Versão 0.32. Campinas: Embrapa Informática Agropecuária, 2012. 1 CD-ROM.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 12. | | IDE, F. H.; VISOLI, M. C.; YAMAGISHI, M. E. B.; VACARI, I.; SANTOS, A. D. dos; QUEIROS, L. R.; COSTAS, I. R. S.; JOSÉ, S. C. B. R.; PÁDUA, J. G. Alelo - Gestor Integrado de Recursos Genéticos - Processo de Monitoração da viabilidade das sementes armazenadas na coleção Colbase. Versão 0.32. Campinas: Embrapa Informática Agropecuária, 2012. 1 CD-ROM.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 15. | | IDE, F. H.; VISOLI, M. C.; YAMAGISHI, M. E. B.; VACARI, I.; SANTOS, A. D. dos; QUEIROS, L. R.; COSTAS, I. R. S.; JOSÉ, S. C. B. R.; PÁDUA, J. G. Alelo - Gestor Integrado de Recursos Genéticos - Serviços de apoio à Gestão da Conservação de Longo Prazo à -20o C. Versão 0.32. Campinas: Embrapa Informática Agropecuária, 2012. 1 CD-ROM.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 20. | | OLIVEIRA, S. R. de M.; ALMEIDA, G. V.; SOUZA, K. R. R.; RODRIGUES, D. N.; NESHICH, G.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G. An integrated database of structural parameters for protein analysis. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster B-44. Na publicação: Stanley R. M. Oliveira, Paula R. Kuser-Falcão, Edgard H. Santos.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 233 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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