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

Abstract

ABSTRACT. 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. We described a pipeline that was able to recover more than 96% of the sequenced genome in a single run and could be helpful for further assembly attempts of other DENV genomes, as well as other RNA virus-like genomes.

Co-Infection of Dengue Virus by Serotypes 1 and 4 in Patient From Medium Sized City From Brazil

“…The F49L substitution perceived in DENV-4 C protein and recognized only in other Brazilian isolates 1,9,35,40 can be considered a genetic signature of Brazilian isolates and needs further investigation.…”

Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses

“…The WEGO program ( Ye et al, 2006 ) was used to classify all of the unigenes based on the GO annotation information. For removing possible contaminants from the transcriptome, we firstly filtered the contaminant sequences by BLAST searches and removed the non-green plant sequences (microbial and human contamination) based on the annotated categories in the KEGG and GO databases ( Gray et al, 2010 ; Casseb et al, 2012 ). Secondly, we detected the candidate genes involved in terpenoid biosynthesis, FA biosynthesis, and response to abiotic stress, which are expressed in three of the libraries.…”