Comparative analysis, genomic analysis of infectious bacteria

Question

[Nitha]

Hi All, I am facing problem how to group the different types of strains and select representative strain to study. Eg: for chlamydia there are three human biovars and they are further listed into 1 to 15 serovars based on ompA gene (outer membrane protein) and each serovars contains different strains. This organism have totally 126 different strains deposited in Ensembl. So when we need to study about all 126 strains it takes long time. Results analysis, graphs genrating will be in huge number. So how to simplify this problem, how can I take representative strains from each serovars? One way is to filter the strain based on the annotation of genome, we could take strains contain only complete annotated genomes. Can anyone give best solution for this type of problem.. Thanks in advance..

Answer 1

[Charles Yin]

If you intend to compare the relationship/similarity of large long genome sets, you may consider to employ alignment-free methods. Alignment-free methods can handle large data set of long lengths and give accurate comparison if you do not need to check which positions are mismatched. For example, you can check this paper and its programs. [ Yin, C., & Yau, S. S. T. (2015). An improved model for whole genome phylogenetic analysis by Fourier transform. Journal of Theoretical Biology. doi:10.1016/j.jtbi.2015.06.033] [https://www.mathworks.com/matlabcentral/fileexchange/52072][1]