| |
|
|
|
Registro Completo |
|
Biblioteca(s): |
Embrapa Café. |
|
Data corrente: |
18/11/2020 |
|
Data da última atualização: |
18/11/2020 |
|
Tipo da produção científica: |
Resumo em Anais de Congresso |
|
Autoria: |
PADILHA, L.; CAIXETA, E. T.; SILVA, F. R. da. |
|
Afiliação: |
LILIAN PADILHA, CNPCa; EVELINE TEIXEIRA CAIXETA MOURA, CNPCa; FELIPE RODRIGUES DA SILVA, CNPTIA. |
|
Título: |
Comparing methods of RNAseq analysis for species without a reference genome. |
|
Ano de publicação: |
2012 |
|
Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTACIONAL BIOLOGY, 8., 2012, Campinas, São Paulo. Resumos... Campinas, SP, 2012. |
|
Idioma: |
Inglês |
|
Notas: |
X-MEETING. |
|
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. |
|
Thesagro: |
Coffea Arábica; Genoma. |
|
Thesaurus Nal: |
Transcriptome. |
|
Categoria do assunto: |
-- |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/217932/1/2012-Resumo-Xmeeting.pdf
|
|
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
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Café (CNPCa) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
URL |
Voltar
|
|
|
| Registros recuperados : 148 | |
| 1. |  | KARAM, D.; MAGALHAES, P. C.; PADILHA, L. Adição de polímeros na viabilidade, vigor e longevidade de sementes de milho. In: CONGRESSO NACIONAL DE MILHO E SORGO, 26.; SIMPÓSIO BRASILEIRO SOBRE A LAGARTA-DO-CARTUCHO, SPODOPTERA FRUGIPERDA, 2.; SIMPÓSIO SOBRE COLLETOTRICHUM GRAMINICOLA, 1., 2006, Belo Horizonte. Inovação para sistemas integrados de produção: resumos. Sete Lagoas: ABMS: Embrapa Milho e Sorgo, 2006. p. 572.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Milho e Sorgo. |
|    |
| 18. | | GARCIA, A. L. A.; GARCIA, A. W. R.; PADILHA, L.; REIS JUNIOR, R. P.; SOUZA, T. Aplicação de uréia com inibidor de urease em mudas de cafeeiro. In: Simpósio de Pesquisa dos Cafés do Brasil, 5., 2007, Águas de Lindóia. Anais. Brasília, D.F. : Embrapa Café, 2007.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Café. |
| |
| 19. | | PADILHA, L.; LOPES, M. M.; VIEIRA, M. G. G. C.; GUIMARAES, C. T. Análises de microssatélites em bulk e perfis genéticos para híbridos de milho. In: CONGRESSO NACIONAL DE MILHO E SORGO, 25.; SIMPOSIO BRASILEIRO SOBRE A LAGARTA-DO-CARTUCHO, SPODOPTERA FRUGIPERDA, 1., 2004, Cuiabá, MT. Da agricultura familiar ao agronegócio: tecnologia, competitividade e sustentabilidade: [resumos expandidos]. Sete Lagoas: ABMS: Embrapa Milho e Sorgo; Cuiabá: Empaer, 2004. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Milho e Sorgo. |
| |
| Registros recuperados : 148 | |
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
