[Genome] Questions on axtNet alignments

[Hiram Clawson]

Good Morning Fuhong:

You can read about the chain and net process in the paper:
	http://www.pnas.org/cgi/content/full/100/20/11484
Evolution's cauldron: Duplication, deletion, and
rearrangement in the mouse and human genomes
W. James Kent, Robert Baertsch,
Angie Hinrichs, Webb Miller, and David Haussler
PNAS | September 30, 2003 | vol. 100 | no. 20 | 11484-11489

And more discussion in the genomewiki:
http://genomewiki.ucsc.edu/index.php/Chains_Nets
http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

--Hiram

Fuhong He wrote:
> Dear sir,
> 
> To our knowledge, the axtNet file axtNet/chr21.hg18.mm9.net.axt provides the chained and netted alignments of the best chain (hg18.mm9.all.chain.gz).  But we noticed that a chain was segmented into small axtNet alignments. What is the criteria you used to segment the chain? Is this done by netToAxt  programme?
> 
> Thank you for your any help!
> 
> Best regards!
> 
> 
> Yours sincerely,
> Fuhong