[Genome] Help!

[Kate Rosenbloom]

Hello WenXin Zheng,

If you want to obtain pairwise alignments for the human genome
vs. other species in our conservation track, you can do this
by downloading the pairwise alignments we used to create the multiple
alignment, which are available here:

http://hgdownload.cse.ucsc.edu/downloads.html#human

These alignments are single-coverage (best alignments of
other genome to human), that result from our chaining & netting
processes applied to the blastz alignments.

An alternative is to extract the pairwise alignments from
the multiple alignment. You can do this by downloading
the multiple alignment, eg. from:

http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way/

together with some simple scripting to filter the file.
Another option is to use  the Galaxy tool provided by
the Penn State bioinformatics group -- there is a link
to Galaxy from the menu bar on the Genome Browser home page.

Blastz is developed and supported by the Penn State group:
     http://www.bx.psu.edu

At UCSC we perform whole-genome blastz alignments on our high-performance
computing clusters.   If you want to align your own sequences in
your local environment, you will want to download the blastz
package from Penn State.  They may also have suggestions regarding
hardware configuration.

     Hope this helps,
	Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics

ZhengWenXin wrote:
> Dear Prof.,
>        Would you please help me to resolve a problem about the conservation track of the UCSC genome browser?
>        I’m interested in the conservation of the human genome with other species. As described in the Methods part, pairwise alignments with the human genome were generated for each species using blastz from repeat-masked genomic sequence. For example, how can I get the best alignment of the human genome and the mouse genome? If I use the blastz software to do it on a PC, how long it will take? Would you please give me an estimate? And I also want to know you hardware environment in which you perform the pairwise alignments. 
>        Thank you very much! Your help will be greatly appreciated.
> Best wishes,
> WenXin Zheng
>  
>  
>  
>  
> Wen-Xin Zheng, PhD candidate
> Bioinformatics Center
> Tianjin University
> Tianjin 300072
> China
> Fax: +86-22-27402697
> Website: http://tubic.tju.edu.cn
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