Hi Everyone, I have three draft genomes (non model organisms) of a species of insect. All three draft genomes represent the same species from three different geographical locations, where this insect behaves differently in all three regions. I have predicted gene sequences from all three and would like to perform a comparative analysis of all the three sets of gene sequences to find out the percent similarity/differences etc among all three, and the gene sequences contributing to the differences. Each set of predicted genes is composed of ~13,000 gene sequences. I would also like to perform a whole genome comparative analysis of all three draft genomes (predicted genome sizes ~400Mb).
For the predicted gene sequences, which tool would be suitable for me to use? One of the tools I would like to try is OrthoVenn. However, since it's designed for comparison and annotation of orthologous gene clusters among multiple species, would it be wise to use it to compare gene sequences from the same species?
Which tool would be advisable to use for the whole genome comparative?
Any suggestions and/or directions will be highly appreciated. Thank you.
If you have three genome from the same species, synteny should be a good way of finding orthologous sequences. Reciprocal best blast hits would also work well, probably.