[Genome] human hg18 alignments to chimpanzee panTro2

[Kate Rosenbloom]

Hello Erika,

The panTro2 chimp chains in our hg18 human browser were indeed
produced by swapping chains derived from a blastz
alignment of hg18 sequence to panTro2.

The parameters used for this alignment were:

blastz.v7 Y=15000  T=2  M=40000000  O=600  H=2000  K=4500  E=150

matrix 
90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90

The hg18 browser multiz was generated before the panTro2
assembly was available, so it is based on hg18/panTro1
pairwise alignments.

    Cheers,
	Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics


Erika wrote:
> 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 <mailto:kvik at bx.psu.edu>
>