Protein sequence analysis of the Zika virus and the dengue virus using Smith Waterman algorithm

Abstract

Zika virus that became a hot issue in the media recent years behind is very interesting to study, especially the Zika virus has similar to infection to Dengue fever. The virus that is infect to humans through mosquito bites by Aedes genus, Especially Aedes aegypti is identical mosquito that spread Dengue, yellow fever and chikungunya. In Brazil, an increase syndrome Zika virus infection in the community have observed by local health authorities, and also in northeast Brazil an increase of microcephaly condition in babies born. In addition, the Zika virus sporadic infection has reported by approximately 13 Americas countries that show very rapid expansion, and also Indonesia, the euphoria discussed increasingly after the positive patient infected by Zika virus has discovered in Jambi on January 2016. Moving on from this, the authors wanted to know how the sequences protein Zika virus when compared with the Dengue virus, the percentage of identical sequence and also the calculation of local alignment its using the Smith Waterman algorithm. In addition it will also be known genetic mutations that occur in Zika virus from its origin until Zika virus into Indonesia and phylogenetic tree spread of the virus to get to Jambi. So the researcher construct sequence alignment tools by using graphical user interface in MATLAB program based on Smith Waterman algorithm, and also a link in the system with the browser as an option for online data retrieval. From the result of sequence alignment by MATLAB and BLAST, that the identical values of sequence using MATLAB is higher than BLAST values. Likewise, the duration of computation that MATLAB computation is more effective than BLAST computation.