I work on non-model insect genomes. In order to look for orthologous regions across species I have had been blasting in the past. But I needed something more robust. I used the online version of mVista and that has been helpful but was recently advised to use liftover. Realised that I needed chain files for the same. However, when I reached out to UCSC they said they cannot make chain files for invertebrate genomes. So any help in making chain files for liftover will be appreciated? Or any help in finding orthologos non-coding regions across species will be appreciated.
My problem more specifically: I am trying to find orthology/synteny of 200kb region across multiple species for which I have the ATAC peaks of in order to look for similar reg-regions.