Hi: I would like to replicate the results of the paper: Versatile and open software for comparing large genomes. In this paper the authors test the Mummer with complete genomes. The problem is when I compare the complete genomes of the A. nidulans and A. fumigatus. I know that when comparing those and because their closeness the results from the dotplot should be almost a perfect diagonal, but this does not happen. Anybody does know how to compare these genomes? Should I compare only chromosomes from both Fungi? From where do you actually recommend to download those genomes? Thanks
Thanks for your help, in the page that you told me http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html which of all the files gives me the complete genome? it is the one that it says Gene downloads, genes.fasta?
You're probably looking for the supercontigs, because that is as close to whole chromosomes as you are going to get. It all depends on your end goal of this exercise.
Perhaps before you embark on whole genome alignments, you should figure out what exactly you want to do, then you can start to plan each step of the analysis -- know what data you will need and what you want to do with it.