I am interested in a relatively small region (~2Mb) of chromosome 1 of the mouse genome (mm9). I would like to create a figure that draws the relationship between this mouse region and the corresponding homologous regions in human. In addition, it would be nice to know the human homology for each of the ~60 mouse genes in this regions. So far, I have played with the NCBI "Map Viewer" with little satisfaction. Could some recommend an appropriate tool?
I would definitely have a look at the MizBee synteny browser by Miriah Meyer. For a video, see http://people.seas.harvard.edu/~miriah/projects/mizbee_small.mov The software itself can be found at http://people.seas.harvard.edu/~miriah/mizbee/Overview.html
I haven't used this software myself (have not been working on that kind of data for a long time), but Miriah is one of the big names in biological data visualization and delivers great work.
A while back, I (and Haibao Tang) wrote gobe (name doesn't mean anything) to do this. 2MB might be a bit large, but you could try, or do it piecewise. You can see an example here: http://synteny.cnr.berkeley.edu/gobeapp/?locs=sorghum_v1.4..1..61840147..61850996&locs=rice_v6..3..10282728..10292920&locs=brachy_v1..Bd1..64381503..64391410&
It's interactive, so if you shift-click in the row with the orange blocks, it will connect to the corresponding HSP in the other track. And you can click on the genes to see there annotation (yay flash)
You can read more about it in the applications note here.
If you data is in BLAST tab-delimited format (8 columns) you should be able to paste it into the box here: http://try-gobe.appspot.com/ and see and interact with your region.
It's a small flash movie so you can host it on your own for more flexibility. Pretty thorough docs and source on github: https://github.com/brentp/gobe/
Check out 'circos' developed by Martin Krzywinski at the BC Genome Sciences Centre.
It's perl-based, so it might take a bit of cpan work to get the dependencies installed, but they're not too bad. It produces extremely high-quality graphics in .png or .svg.
There is an extensive tutorial here:
Here is an example that compares Human to 7 other species: