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.

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.cse.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.cse.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.cse.ucsc.edu/goldenPath/mm9/liftOver/ .
For a single file, e.g. mm8ToHg18.over.chain.gz
    rsync -avzP \
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/liftOver/mm9ToHg18.over.chain.gz .

Or with wget, all files:
    wget --timestamping \
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/liftOver/*'
With wget, a single file:
    wget --timestamping \
        'ftp://hgdownload.cse.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 2013-03-21 17:15 2.7K 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 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