Working with synteny blocks of dierent resolution

MGRA has troubles in genomic regions of high breakpoint reuse; we plan to eliminate these troubles by locally increasing resolution in such regions. Our goal is to increase the accuracy of MGRA tool. Synteny blocks of low resolution tend to be more reliable then high resolution blocks, but we may miss multiple evolutionary event while working with low resolution blocks only. So what we want is to detect MGRA's problem regions and insert blocks of high resolution into adjacencies of low resolution and create a new set of synteny blocks of different resolution that we want to use in the rearrangement history reconstruction with the help of MGRA.