플라비 바이러스

Today Zika virus is being a very big problem. In Brazil, more than 1.5 million people have become infected since April, 2015. The Zika virus was first found in Uganda in 1947 [1, 2]. As time goes by, zika virus arose in many countries like Malaysia, Micronesia, and Tahiti island in the South Pacific. Now, in recent 2 months, Zika virus has been found in about 39 countries. And, because of zika virus, few people died [3]. Not only Zika virus, but also other viruses (like west nile virus, yellow fever, tick borne encephalitis, and dengue virus) are fatal to people. And all of them belong to flavivirus. Unfortunately, there is no specific treatment of the viruses. Actually, vaccines exist for yellow fever and dengue virus [4, 5] but other viruses (west nile virus, tick borne encephalitis, and zika virus) don't have vaccine. And treatments are only relief from symptoms. This is why we are doing this experiment. An investigation on figuring out similarities and differences between the viruses and yellow fever may lead us to have a deeper understanding about the viruses. By using apriori algorithm and decision tree, we are able to expect to find out the possibility of a treatment that is effective to them.

 

 

https://www.matec-conferences.org/articles/matecconf/pdf/2016/32/matecconf_iccpe2016_01005.pdf

 

 

Nowadays, zika virus infection-occurred in Brazil-is becoming serious global problem. Temporary treatments-using drug-can alleviate symptoms for a while but cannot be a basic solution for infections. We researched amino acids of Zika virus and other four kinds of flaviviruses-Dengue fever, Yellow fever, Saint Louis, Japanese Encephalitis-with bioinformatic experiment; Apriori, K-means and Decision Tree algorithm. Results show differences and common things among them-Japanese Encephalitis has most representative amino acid.

 

https://ieeexplore.ieee.org/document/7890130

Comparison of flavivirus using datamining-Apriori, K-means, and decision tree algorithm

 

 

 

뎅기 FASTA

 

https://www.ncbi.nlm.nih.gov/protein/ABG75765.1?report=fasta 

polyprotein [dengue virus type I] - Protein - NCBI

 

 

황열병 FASTA

https://www.ncbi.nlm.nih.gov/protein/QHB50164.1?report=fasta 

polyprotein [Yellow fever virus] - Protein - NCBI

 

 

일본뇌염 FASTA

https://www.ncbi.nlm.nih.gov/protein/ABU94627.1?report=fasta 

polyprotein [Japanese encephalitis virus] - Protein - NCBI

 

Tick-borne encephalitis virus

https://www.ncbi.nlm.nih.gov/protein/AEQ77280.1?report=fasta 

polyprotein [Tick-borne encephalitis virus] - Protein - NCBI

 

 

지카 바이러스 

https://www.ncbi.nlm.nih.gov/protein/BCJ78252.1?report=fasta 

polyprotein [synthetic Zika virus] - Protein - NCBI

 

 

 

ABU94627.1
BCJ78252.1

 

일본뇌염과 지카바이러스의 유사성 비교를 해 보았습니다. 

 

 

결과를 보니 많이 다릅니다. 

Identities  56% - 서로 간의 일치성이 56% 정도입니다.

Positives 74% - 일치하는 아미노산들의 성격을 고려할 때 어느 정도 유의하게 나타나는 것에 대한 결과 

Gaps 0% - 공백 스코어는 1% 미만이라는 뜻입니다. 

 

 

이제 5개의 바이러스 서열을 NCBI에서 다운로드하여서 Blast와 Mega-11에서 실습해 봅시다. 

각각의 결과를 보고 어떤 결과가 나오는지와 결과가 다른 이유에 대해 설명해 봅시다.

 

바이러스 간의 일치성은 얼마이며 계통수에서 가장 가까운 바이러스는 무엇인지 알아봅시다.