[Genome] A question about liftover program

[Brooke Rhead]

Hello Shan,

I apologize for the delay in answering your question.

This is indeed a problem that other users have encountered, and a page 
has been created on our wiki site with instructions for creating 
liftOver chain files:

http://genomewiki.cse.ucsc.edu/index.php/Minimal_Steps_For_LiftOver

The wiki page above uses tools in the Genome Browser source code.  See 
this link for downloading the source if you have not already done so:

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

There is also some discussion of creating liftOver chains in the mailing 
list archives:

http://www.soe.ucsc.edu/pipermail/genome-mirror/2007-June/000509.html

I hope this information is helpful.  Please feel free to write back to 
the mailing list if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Shan Yang wrote:
> Dear Genome Browser
> 
> I am studying a microbial genome that hasn't been fully annotated. It
> is a substrain of E.Coli K12, which is annotated. Since they are very
> similar in sequence, I would like to use the K12 annotation for my
> genome for now. It looks like that liftover program is very suitable
> for such task. But the problem is that I don't have the chain files
> between the two strains to run liftover. I am wondering if I can get
> some idea how to generate such chain files from two fasta files of my
> microbial genome and K12. I think it is a quite general problem many
> researchers may run into. So it will be great if you can provide such
> program on the website.
> 
> Thank you very much!
> 
> Shan
> 
> 
> 
> 
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