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Old 12-12-2012, 09:02 AM   #1
fadista
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Default visualizing differences between gneome builds

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.
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Old 12-12-2012, 09:53 AM   #2
GenoMax
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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?
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Old 12-13-2012, 03:50 AM   #3
fadista
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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...
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Old 12-13-2012, 08:12 AM   #4
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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.
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Old 12-16-2012, 06:50 AM   #5
fadista
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Perfect. Thanks a lot for Mauve
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