I want to do some realignment of a segment of the genome that show conservation between different species (human, zebrafish, mouse, rat,etc). I know the genomic coordinate of the human region and if I just view the region on human in UCSC genome browser, i can see the Multiz sequence alignment track. What I need is a way to extract the sequences that contribute to the sequence alignment in the view range. I looked around but couldn't find a function to do this. I'm wondering what's the traditional way of doing this?
I can think of using liftover to find corresponding syntenic regions of the human sequence and do this for each species. Is this the right way to go? Are there some tools out there that can do it more efficiently?