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Registro Completo |
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Biblioteca(s): |
Embrapa Café. |
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Data corrente: |
18/11/2020 |
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Data da última atualização: |
18/11/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
PADILHA, L.; CAIXETA, E. T.; SILVA, F. R. da. |
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Afiliação: |
LILIAN PADILHA, CNPCa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa; FELIPE RODRIGUES DA SILVA, CNPTIA. |
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Título: |
Comparing methods of RNAseq analysis for species without a reference genome. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTACIONAL BIOLOGY, 8., 2012, Campinas, São Paulo. Resumos... Campinas, SP, 2012. |
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Idioma: |
Inglês |
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Notas: |
X-MEETING. |
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Conteúdo: |
New sequencing technologies brought deep probing of transcriptomes (so-called RNAseq) to the reach of individual researches. Analysis of RNAseq sequences, however, depend on the alignment of reads to a reference genome. Some approaches have been proposed to allow de novo assembly of the transcripts, therefore allowing RNAseq to be used on organisms lacking a reference genome. The efficiency of those approaches, however, were tested only with diploid species. Here we propose a methodology to evaluate the results of de novo assembly of allotetraploid Coffea arabica RNAseq reads obtained from libraries of coffee leaves infected by Hemileia vastatrix. Trinity was able to assemble longer transcripts when compared to ABySS, SOAPdenovo and Oases. Moreover, the transcripts assembled by Trinity where more similar to the ones obtained using Cufflinks after aligning the RNAseq to 10 Coffea sp. publically available BAC sequences. Comparison of the most abundant transcripts with several Coffea sp. single copy described genes, though, shows that all assemblers failed to perfectly reconstruct the transcripts. |
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Thesagro: |
Coffea Arábica; Genoma. |
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Thesaurus Nal: |
Transcriptome. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/217932/1/2012-Resumo-Xmeeting.pdf
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Marc: |
LEADER 01751nam a2200181 a 4500
001 2126751
005 2020-11-18
008 2012 bl uuuu u00u1 u #d
100 1 $aPADILHA, L.
245 $aComparing methods of RNAseq analysis for species without a reference genome.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTACIONAL BIOLOGY, 8., 2012, Campinas, São Paulo. Resumos... Campinas, SP$c2012
500 $aX-MEETING.
520 $aNew sequencing technologies brought deep probing of transcriptomes (so-called RNAseq) to the reach of individual researches. Analysis of RNAseq sequences, however, depend on the alignment of reads to a reference genome. Some approaches have been proposed to allow de novo assembly of the transcripts, therefore allowing RNAseq to be used on organisms lacking a reference genome. The efficiency of those approaches, however, were tested only with diploid species. Here we propose a methodology to evaluate the results of de novo assembly of allotetraploid Coffea arabica RNAseq reads obtained from libraries of coffee leaves infected by Hemileia vastatrix. Trinity was able to assemble longer transcripts when compared to ABySS, SOAPdenovo and Oases. Moreover, the transcripts assembled by Trinity where more similar to the ones obtained using Cufflinks after aligning the RNAseq to 10 Coffea sp. publically available BAC sequences. Comparison of the most abundant transcripts with several Coffea sp. single copy described genes, though, shows that all assemblers failed to perfectly reconstruct the transcripts.
650 $aTranscriptome
650 $aCoffea Arábica
650 $aGenoma
700 1 $aCAIXETA, E. T.
700 1 $aSILVA, F. R. da
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Registro original: |
Embrapa Café (CNPCa) |
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| Registros recuperados : 169 | |
| 6. |  | SALES, R. M. O. B.; SILVA, F. R. da. FishEST: a tool that mines est libraries for genes differentially expressed. In: ANNUAL MEETING OF THE SBBq, 36.; IUBMB CONFERENCE, 10., 2007, Salvador, BA. Infectious diseases: biochemistry of parasites, vectors and hosts: program and abstracts. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2007.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 11. | | VINECKY, F.; RODRIGUES, G. C.; SILVA, F. R. da; ANDRADE, A. C. Análise da expressão gênica da parte aérea de cafeeiro em condições de déficit hídrico. ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENETICOS E BIOTECNOLOGIA, 8., 2003, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2003. p. 29| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 12. | | VINECKY, F.; BRITO, K. M. de; SILVA, F. R. da; ANDRADE, A. C. Análise in silico de genes potencialmente envolvidos na resposta aos estresses abióticos, presentes na base de dados do genoma café. In: SIMPÓSIO DE PESQUISA DOS CAFÉS DO BRASIL, 4., 2005, Londrina. Anais... Brasília: Embrapa Café, 2005. 1 CD-ROM. Núcleo: Biotecnologia aplicada à cadeia agroindustrial do café, p. 1.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 15. | | BARBOSA, A. V.; SALES, R. M. O. B.; ANDRADE, A. C.; SILVA, F. R. da. CoffEST: yet another resource for Coffea spp. EST analysis... well, this one is publically available. In: INTERNATIONAL PLANT & ANIMAL GENOMES CONFERENCE, 17., 2009, San Diego, CA. [Proceedings...]. [S. l.: s.n.], 2009. P806| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 20. | | ARAÚJO, M. M. M.; SILVA, F. R. da; MARINHO, V. L.; SOUZA JÚNIOR, M. T. Decodificando o genoma do vírus da "meleira": parte 2. Fitopatologia Brasileira, Brasília, v. 30, p. 164, ago. 2005. Suplemento: CONGRESSO BRASILEIRO DE FITOPATOLOGIA, 38., 2005, Brasília, DF. p. 183.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 169 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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