visualizing differences between gneome builds

[fadista]

Hi,

I know you have the remap tool to map genomic coordinates between different builds, but I was wondering if there is any visualizing tool that I can use to compare the assembly of small region (lets say 2Mb) from two assemblies of the same species.
Thanks.

[GenoMax]

You could open two copies of IGV (or UCSC/Ensembl browser in two web browser windows) and tile them. But I guess you are looking for a tool that can open both builds in the same window?

[fadista]

Yes, I was looking for a software where I was able to detect differences in assembly like duplications, inversions, expansions quite easily in a 2 Mb window or so...

[ajthomas]

If I understand what you're looking for, you might have a look at Mauve. You load your genomes and it gives you a graphical representation of the genomes with boxes and lines drawn to show homology. It really helps visualize genomic rearrangements.

[fadista]

Perfect. Thanks a lot for Mauve