Assembly

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

S. M. M. Casseb, Cardoso, J. F., Ramos, R., Carneiro, A., Nunes, M., Vasconcelos, P. F. C., and Silva, A., Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies, vol. 11, pp. 3688-3695, 2012.

Currently assembling genomes without reference is one of the most important challenges for bioinformaticists all over the world in an attempt to characterize new organisms. The current study has used two dengue virus type 4 (DENV-4) strains recently isolated in Brazil, which have its genomes sequenced using the GSFLX 454 sequencer (Roche, Life Science) by the pyrosequencing method. The GSFLX 454 data were used for testing different genome assembling strategies.

A new set of bioinformatics tools for genome projects

L. G. P. Almeida, Paixão, R., Souza, R. C., da Costa, G. C., de Almeida, D. F., and de Vasconcelos, A. T. R., A new set of bioinformatics tools for genome projects, vol. 3, pp. 26-52, 2004.

A new tool called System for Automated Bacterial Integrated Annotation - SABIA (SABIÁ being a very well-known bird in Brazil) was developed for the assembly and annotation of bacterial genomes. This system performs automatic tasks of assembly analysis, ORFs identification/analysis, and extragenic region analyses. Genome assembly and contig automatic annotation data are also available in the same working environment.

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