Selected topic:
Sequence alignment
Review of Journal article:
Title: Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus
Author: Zhen Xia, Gulei Jin, Jun Zhu and Ruhong Zhou
Bioinformatics, Vol. 25, no.18, 2009, pages 2309-2317
Mapping of antigenic and genetic evolution pathways of Influenza A is important in vaccine development and prevention of the virus outbreak. Study of 4000 A/N3H2 Hemagglutinin (HA) sequences from 1968 to 2008 was done to model the evolutionary path of the virus, and to identify potential mutations in the future. The mutual information method was used to diagnosis the co-occurring mutations and correlations between each amino acid sites of N3H2 HA sequences, and to form a site transition network (STN). The effectiveness and accuracy of STN is compatible with phylogenetic tree and antigenic maps, with reduced cost.
The study indicates 63 out of 312 sites of the HA sequences have high interactions among themselves. STN demonstrates these 63 sites and their clear trajectories on modeling the antigenic transition during the evolution of Influenza. The study shows that the probability for a site to mutate to a new amino acid that did not happen before is low, and mutations have strong preference of mutation sites. Study of historical mutations allows the author to predict the future mutations, which possibly produce the next antigen change and the resultant amino acid of the new strain. With this information, predictions were made for each year of 1999-2008. The accuracy of the prediction is approximately 70% in average. Clustering was performed to reveals information on different simultaneous multi-site mutation in antigenic drifts. Prediction for year 2009-2010 was made. It requires time to prove its accuracy. In this study, locations, seasons, new vaccine and other pressure have not taken into accounts. Future study should be made with consideration of these pressures.
Research question and objectives:
Is one vaccine enough for all human races of the world?
Use sequence alignment to analyze 2 sets of H3N2 HA sequences of 2 different human races/ continents and see if there is any difference in them.
Are there any hurdles for applying sequence annealing in MSA of DNA sequences?
回覆刪除Or it is just a straight-forward approach?
If it can be directly applied without further investigation, the project is not well justified.
It is a very interesting project.
回覆刪除If the data collection is feasible, please go ahead to proceed to the next steps.