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

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.

mouse assembly genomics
• 3,789 views • link
updated by Ram Ram • written by Ahdf-Lell-Kocks • Ahdf-Lell-Kocks

2 answers

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

• 1 views • link
written by Zev.Kronenberg Zev.Kronenberg

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

• 0 views • link
updated by Ram Ram • written by andrese52 • andrese52

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.

• 0 views • link
written by chitoboy • chitoboy

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.

• 2 views • link
written by brentp brentp

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