[Genome] human hg18 alignments to chimpanzee panTro2

[Erika]

Dear colleagues at Santa Cruz Genome Browser,

I am a grad student working with Kateryna Makova at Penn State  
University and we're interested in using the new hg18 alignments to  
chimp (panTro2).

I noticed from the description in http://hgdownload.cse.ucsc.edu/ 
goldenPath/hg18/vsPanTro2/

	The chainSwap program was used to translate panTro2-referenced  
chained blastz
	alignments to hg18 into hg18-referenced chains aligned to panTro2.  See
	the download directory goldenPath/panTro2/vsHg18/README.txt for more
	information about the panTro2-referenced blastz and chaining process.

I just want to confirm that this is the case: the hg18 vs panTro2  
alignments were constructed by swapping the panTro2 vs hg18 blastz  
output.

Also, I was wondering for the multi-z alignments available if the  
same is true: the pairwise hg18 vs panTro2 were constructed from  
using chainSwap on the output from chimp-referenced blastz.

Since we are interested in comparisons between BAC-derived chimp  
sequence to the whole genome assembly, we would like to align our  
sequences to human using parameters as similar as possible to the  
alignments created for the assembly.  We are therefore interested in  
how the alignments of hg18 to panTro2 were created.  If you could  
help us with this information we would greatly appreciate it.

Thanks for the help!
Sincerely,
Erika Kvikstad

**********************************************************
E.M. Kvikstad
Academic Computing Fellow
IGDP Genetics
Center for Comparative Genomics and Bioinformatics
The Pennsylvania State University
208 Mueller Lab
University Park, PA 16802
(814) 863-2185
kvik at bx.psu.edu