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1.
Biol Res ; 49(1): 39, 2016 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-27605096

RESUMO

BACKGROUND: New sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes. FINDINGS: Three different assembly softwares (ABySS, Ray and SPAdes) were tested for their ability to correctly assemble the full-length of viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig. CONCLUSIONS: The proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.


Assuntos
RNA Polimerases Dirigidas por DNA/genética , Genoma Viral , Técnicas de Amplificação de Ácido Nucleico/métodos , RNA Viral , Análise de Sequência de RNA/métodos , Montagem de Vírus , Alphavirus/genética , República Centro-Africana , Biologia Computacional , Mapeamento de Sequências Contíguas , Mengovirus/genética , Valores de Referência , Reprodutibilidade dos Testes , Software
2.
Biol. Res ; 49: 1-8, 2016. ilus, graf, tab
Artigo em Inglês | LILACS | ID: biblio-950865

RESUMO

BACKGROUND: New sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes. FINDINGS: Three different assembly softwares (ABySS, Ray and SPAdes) were tested for their ability to correctly assemble the full-length of viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig. CONCLUSIONS: The proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.


Assuntos
RNA Polimerases Dirigidas por DNA/genética , RNA Viral , Genoma Viral , Análise de Sequência de RNA/métodos , Montagem de Vírus , Técnicas de Amplificação de Ácido Nucleico/métodos , Valores de Referência , Software , República Centro-Africana , Reprodutibilidade dos Testes , Alphavirus/genética , Mengovirus/genética , Biologia Computacional , Mapeamento de Sequências Contíguas
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