Hi, I'm trying to infer orthologous regions between two different species using the chain and/or net file provided by UCSC. To understand how to do this, I decided to use a well conserved region (the HOXA cluster from human genome) as inquiry. This region's coordinate (panning from HOXA1 to HOXA13) is chr7:25681793-25788913 in hg19. Due to HOX genes' high conservation level, I expect there to be a corresponding region in the Chimp genome.
To check whether this is indicated by the chain/net files, I downloaded the hg19.panTro3.rbest.chain and hg19.panTro3.rbest.net files. For some reason, I didn't locate any chain/net that overlap with the aforementioned region although if I input the said region on genome browser and turned on the comparative genomics track. it seems that the Chimp Alignment Net does exist for this region. I suspect that I may have some fundamental misunderstanding about the files of interest and I also am not very clear about the practical difference between the rbest.chain and rbest.net files. Your input will be greatly appreciated. Best, - Jia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
