Pairwise Genome Alignment To Account For The Differences Between Two Mouse Assemblies?

Question

[Ahdf-Lell-Kocks]

There is a new mouse genome assembly available:

http://www.ncbi.nlm.nih.gov/genome/assembly/327618/

and I would like to know what would be a good method to do the pairwise alignment of this assembly versus de previous one to have an account of the differences.

Answer 1

[Zev.Kronenberg]

If your interested in looking at synteny you can use LASTZ and then visualize the results in circos.

[andrese52]

Hi Zev, this is my first time using circos and LASTZ. Now I have the file out.maf from LASTZ. How to use it as an input in circos? I just want a quick guide how to input this file in the circos.conf file and get the alignment. I can play around with the program from there and get results.

Thank you

[chitoboy]

Hi andrese52,

Were you able to figure out how to visualize the out.maf from LASTZ on circos? I am in the same situation as you were. Please let me know. I would really appreciate you help. Thank You.

Answer 2

[brentp]

You can follow the UCSC pipeline using BLAT to create .chain files that map between assemblies (and contain the differences you're looking for). Then use their liftOver tool to convert.

See this page for a starting point.