[Genome] conversion of genome coordinates between genome assemblies

[Ann Zweig]

Hello Bogdan,

	The LiftOver tool on the website will help you with this task.  This 
tool converts genome coordinates and genome annotation files between 
assemblies.  The input data can be pasted into the text box, or uploaded 
from a file.  You will find the tool here: 
http://genome.ucsc.edu/cgi-bin/hgLiftOver

	There is no direct lift from mm7 to mm9, but you can do a double-lift: 
first from mm7 (Aug 2005) to mm8 (Feb 2006), then from mm8 to mm9 (July 
2007).

	Paste all of your input (predicted binding site locations) into the 
large text box in either position format (e.g. chr1:111111-222222) or 
BED format (e.g. chr1 111111 222222 itemName).

	I hope this information is helpful to you.  Please don't hesitate to 
contact the mail list again if you require further assistance.	

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Bogdan Tanasa wrote:
> Hello hello. I would like to have your suggestions on the following:
> 
> I do have a set of predicted binding sites of transcription factors in
> mouse genome assembly 2005 (mm7). I would like to have the
> coordinates of the predicted binding sites in mouse mm9 assembly.
> 
> I am looking for an efficient and quick way to convert the coordinates
> between these mouse genome assemblies. I would appreciate your
> suggestions. Thanks !
> 
> Bogdan
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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