This directory contains a dump of the UCSC genome annotation database for
the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome
(mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2))
from the Mouse Genome Sequencing Consortium.

The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Mouse Genome Sequencing Consortium,
and the National Center for Biotechnology Information (NCBI).
For more information on the mouse genome, see the project website:

See also: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
          http://www.ncbi.nlm.nih.gov/genome/52

Files included in this directory (updated nightly):

  - *.sql files:  the MySQL commands used to create the tables

  - *.txt.gz files: the database tables in a tab-delimited format
    compressed with gzip.

To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
  http://genome.ucsc.edu/cgi-bin/hgTables?db=mm10
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

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If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/mm10/database/. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

To uncompress the *.txt.gz files:
    gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.

To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql mm10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql mm10 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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All the files and tables in this directory are freely usable for any purpose,
except for the Swiss-Prot/UniProt data in knownGene.txt, which has the
following terms of use:

UniProt copyright (c) 2002 - 2004 UniProt consortium

For non-commercial use all databases and documents in the UniProt FTP
directory may be copied and redistributed freely, without advance
permission, provided that this copyright statement is reproduced with
each copy.

For commercial use all databases and documents in the UniProt FTP
directory, except the files

ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz

and

ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz

may be copied and redistributed freely, without advance permission,
provided that this copyright statement is reproduced with each copy.

More information for commercial users can be found in:
http://www.expasy.org/announce/sp_98.html

From January 1, 2005, all databases and documents in the UniProt FTP
directory may be copied and redistributed freely by all entities,
without advance permission, provided that this copyright statement is
reproduced with each copy.

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This file last updated: 2012-02-09 - 09 February 2012
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