Question: Drawing Homology Between Mouse And Human
6
gravatar for Aaronquinlan
7.5 years ago by
Aaronquinlan10k
United States
Aaronquinlan10k wrote:

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?

homology visualization • 3.6k views
ADD COMMENTlink written 7.5 years ago by Aaronquinlan10k
6
gravatar for Jandot
7.5 years ago by
Jandot370
GB
Jandot370 wrote:

Hi there,

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.

jan.

ADD COMMENTlink written 7.5 years ago by Jandot370

That looks incredible. I think I need a drink after watching that video. Great stuff.

ADD REPLYlink written 7.5 years ago by Aaronquinlan10k
3
gravatar for brentp
7.5 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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/

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by brentp23k

This looks nice as well, thanks.

ADD REPLYlink written 7.5 years ago by Aaronquinlan10k
2
gravatar for dfornika
7.5 years ago by
dfornika1000
Vancouver, British Columbia, Canada
dfornika1000 wrote:

Check out 'circos' developed by Martin Krzywinski at the BC Genome Sciences Centre.

http://circos.ca/

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:

http://circos.ca/tutorials/lessons/

Here is an example that compares Human to 7 other species:

http://circos.ca/guide/genomic/img/circos-conservation.png

ADD COMMENTlink written 7.5 years ago by dfornika1000

Do you know of a specific tutorial for using Circos to draw synteny?

ADD REPLYlink written 7.5 years ago by Aaronquinlan10k
1
gravatar for Daniel Swan
7.5 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

Traditionally I might have thought something like ACT appropriate:

http://www.sanger.ac.uk/resources/software/act/

Although Circos is clearly prettier.

ADD COMMENTlink written 7.5 years ago by Daniel Swan13k

Thanks Daniel, I'll give this a try.

ADD REPLYlink written 7.5 years ago by Aaronquinlan10k
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