I'm attempting to do comparative genomics on a gene locus. There is a ~ 100 kb duplication in the C57B/6 strain of mice, but not DBA/2 or BALB/c strains. Is there any way to get the locus sequence in the other strains, or to specify strain when preforming a BLAST analysis?
The Sanger center has sequenced many mouse strains, with some great resources available online at their web site. There you can download and compare C57BL/6, DBA/2J, BALB/cJ, etc. and compare your loci of interest to numerous other strains. You may have to pull down the data you want and set up a local BLAST instance.