I'm completely new in bioinformatics.
I have to compare two strains of bacteria of a newly discovered species to find out why one is growing faster than the other. the two genomes are already sequenced and automatically annotated. I used BRIG, mummer and Mauve to align the genomes and found that they are closely related.
I then used blast to compare the proteins from the two species and find which genes were unique to each genome and I'm currently looking at the role of each of those genes in uniprot.
But now I find myself a bit lost because I have no idea on what I should do next . What should I do to know what gene is responsible for the difference of phenotype?
What should I look for?
Also is there some kind of course that explain the different stage of comparative genomic analyses?
Thank you all in advance for any help you can provide me.