The data files ("UCSC Chain Files") in this directory are property of The
Regents of the University of California, and made available free for
non-commercial use by Independent Researchers and Nonprofit Organizations. Any
other use of UCSC Chain Files requires a commercial license, for which users
should contact genomebrowser@ucsc.edu. As used herein, "Independent
Researcher" means an individual who is autonomous with respect to the
research activities for which he or she uses the UCSC Chain Files (note: such
use does not extend to any use of the UCSC Chain Files at the direction and/or
for the benefit of a for-profit organization); and "Nonprofit
Organization" means a university or other institution of higher education,
or a not-for-profit organization officially recognized or qualified under the
laws of the country in which it is organized or located, or any nonprofit
scientific or educational organization qualified under a federal, state or local
jurisdiction's nonprofit organization statute. Downloading or using UCSC Chain
Files indicates your acceptance of the End User License Agreement (EULA) posted
at "https://genome.ucsc.edu/license/EULA.pdf"; redistribution of UCSC Chain
Files by you must include this README file with these license restrictions, in
the same archive or directory with the chain files.
This directory contains the data files required as input to the
liftOver utility. This tool -- which requires a Linux platform --
allows the mass conversion of coordinates from one assembly to
another. The executable file for the utility can be downloaded from
http://hgdownload.soe.ucsc.edu/admin/exe/
The file names reflect the assembly conversion data contained within
in the format <db1>To<Db2>.over.chain.gz. For example, a file named
mm9ToHg18.over.chain.gz file contains the liftOver data needed to
convert mm9 (Mouse Build 37) coordinates to hg18 (Human Build 36).
If no file is available for the assembly in which you're interested,
please send a request to the genome mailing list
(genome@soe.ucsc.edu) and we will attempt to provide you with one.
To download a large file or multiple files from this directory,
we recommend that you use ftp rather than downloading the files via our
website. To do so, ftp to hgdownload.soe.ucsc.edu (user: anonymous),
then cd to goldenPath/mm9/liftOver. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
-------------------------------------------------------
Please refer to the credits page
(http://genome.ucsc.edu/goldenPath/credits.html) for guidelines and
restrictions regarding data use for these assemblies.
-------------------------------------------------------
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/ .
For a single file, e.g. mm8ToHg18.over.chain.gz
rsync -avzP \
rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/mm9ToHg18.over.chain.gz .
Or with wget, all files:
wget --timestamping \
'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/*'
With wget, a single file:
wget --timestamping \
'ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/liftOver/mm9ToHg18.over.chain.gz' \
-O mm9ToHg18.over.chain.gz
To uncompress the *.chain.gz files:
gunzip <file>.chain.gz
The liftOver utility can read the files in their .gz format,
it is not necessary to uncompress them to use with the liftOver command.
This file last updated: 2007-07-26 - 26 July 2007
Name Last modified Size Description
Parent Directory -
md5sum.txt 2022-10-26 12:05 2.9K
mm9ToAilMel1.over.chain.gz 2010-02-04 18:51 55M
mm9ToAnoCar1.over.chain.gz 2007-09-21 11:57 7.0M
mm9ToAnoCar2.over.chain.gz 2011-04-25 17:45 6.8M
mm9ToBosTau3.over.chain.gz 2007-09-25 22:47 53M
mm9ToBosTau4.over.chain.gz 2008-03-11 23:13 52M
mm9ToBosTau6.over.chain.gz 2011-05-17 10:59 53M
mm9ToBosTau7.over.chain.gz 2012-01-22 18:09 53M
mm9ToBraFlo1.over.chain.gz 2008-04-14 14:08 2.4M
mm9ToCalJac1.over.chain.gz 2007-09-06 20:01 65M
mm9ToCalJac3.over.chain.gz 2010-02-12 20:27 63M
mm9ToCanFam2.over.chain.gz 2007-09-05 02:12 65M
mm9ToCavPor3.over.chain.gz 2008-04-11 18:06 58M
mm9ToDanRer5.over.chain.gz 2007-09-13 21:00 6.4M
mm9ToDanRer6.over.chain.gz 2009-12-18 15:29 6.3M
mm9ToDanRer7.over.chain.gz 2010-12-17 13:11 5.8M
mm9ToEchTel1.over.chain.gz 2007-09-27 11:53 28M
mm9ToEquCab1.over.chain.gz 2007-09-25 07:06 66M
mm9ToEquCab2.over.chain.gz 2009-07-01 12:13 66M
mm9ToFelCat4.over.chain.gz 2010-06-08 17:55 49M
mm9ToFr2.over.chain.gz 2007-09-07 12:14 3.7M
mm9ToGalGal3.over.chain.gz 2007-09-25 10:41 7.4M
mm9ToGasAcu1.over.chain.gz 2007-09-07 15:29 3.9M
mm9ToHg18.over.chain.gz 2007-08-15 11:33 74M
mm9ToHg19.over.chain.gz 2009-05-14 10:40 74M
mm9ToLoxAfr3.over.chain.gz 2009-08-12 20:24 52M
mm9ToMelGal1.over.chain.gz 2011-03-30 09:30 4.5M
mm9ToMm8.over.chain.gz 2007-11-05 17:53 1.2M
mm9ToMm10.over.chain.gz 2012-02-09 12:07 523K
mm9ToMm39.over.chain.gz 2022-10-25 12:50 207K
mm9ToMonDom4.over.chain.gz 2007-09-26 22:15 20M
mm9ToMonDom5.over.chain.gz 2009-08-31 20:20 20M
mm9ToOrnAna1.over.chain.gz 2007-09-25 00:40 12M
mm9ToOryCun2.over.chain.gz 2010-01-15 18:41 51M
mm9ToOryLat2.over.chain.gz 2008-08-27 10:45 4.2M
mm9ToOviAri1.over.chain.gz 2010-04-16 11:51 32M
mm9ToPanTro2.over.chain.gz 2007-09-25 03:12 72M
mm9ToPanTro3.over.chain.gz 2011-03-08 09:49 67M
mm9ToPetMar1.over.chain.gz 2008-04-14 17:18 2.8M
mm9ToPonAbe2.over.chain.gz 2007-09-20 12:35 67M
mm9ToRheMac2.over.chain.gz 2007-09-06 12:10 75M
mm9ToRn4.over.chain.gz 2007-08-14 12:47 70M
mm9ToRn5.over.chain.gz 2013-03-21 10:43 59M
mm9ToSusScr2.over.chain.gz 2010-03-27 01:04 47M
mm9ToTetNig1.over.chain.gz 2007-09-07 12:19 3.7M
mm9ToTetNig2.over.chain.gz 2009-09-15 15:59 3.6M
mm9ToXenTro2.over.chain.gz 2007-09-21 15:53 6.6M
mm9ToXenTro3.over.chain.gz 2011-09-20 17:25 6.5M