This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (BGI CR_1.0/rheMac3) assembly of the rhesus genome (rheMac3,
Beijing Genomics Institute, Shenzhen (GCA_000230795.1)).  The annotations
were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/215
    http://www.ncbi.nlm.nih.gov/genome/assembly/310688
    http://www.ncbi.nlm.nih.gov/bioproject/51409

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=rheMac3
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

---------------------------------------------------------------
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/rheMac3/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/rheMac3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac3/database/gc5BaseBw.txt.gz' 
        -O gc5BaseBw.txt.gz

Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/

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 rheMac3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within 
the scientific community to the most up to date and comprehensive DNA 
sequence information. Therefore, NCBI places no restrictions on the use 
or distribution of the GenBank data. However, some submitters may claim 
patent, copyright, or other intellectual property rights in all or a 
portion of the data they have submitted. NCBI is not in a position to 
assess the validity of such claims, and therefore cannot provide comment 
or unrestricted permission concerning the use, copying, or distribution 
of the information contained in GenBank.

-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
-----------------------------------------------------------------------------
      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2012-11-21 14:34 2.1K all_est.txt.gz 2012-11-21 14:34 3.5M all_mrna.sql 2020-09-01 09:22 2.1K all_mrna.txt.gz 2020-09-01 09:22 16M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.1M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 68 chainCalJac3.sql 2012-11-21 15:09 1.7K chainCalJac3.txt.gz 2012-11-21 15:09 13M chainCalJac3Link.sql 2012-11-21 14:53 1.6K chainCalJac3Link.txt.gz 2012-11-21 14:53 221M chainGorGor3.sql 2012-11-21 14:54 1.7K chainGorGor3.txt.gz 2012-11-21 14:55 218M chainGorGor3Link.sql 2012-11-21 14:50 1.6K chainGorGor3Link.txt.gz 2012-11-21 14:51 646M chainHg19.sql 2012-11-21 15:07 1.7K chainHg19.txt.gz 2012-11-21 15:07 15M chainHg19Link.sql 2012-11-21 14:58 1.5K chainHg19Link.txt.gz 2012-11-21 14:58 168M chainHg38.sql 2015-05-18 07:56 1.7K chainHg38.txt.gz 2015-05-18 07:56 16M chainHg38Link.sql 2015-05-18 07:55 1.5K chainHg38Link.txt.gz 2015-05-18 07:55 176M chainMm10.sql 2012-11-21 14:45 1.7K chainMm10.txt.gz 2012-11-21 14:45 60M chainMm10Link.sql 2012-11-21 14:47 1.5K chainMm10Link.txt.gz 2012-11-21 14:48 474M chainMonDom5.sql 2012-11-21 14:55 1.7K chainMonDom5.txt.gz 2012-11-21 14:56 539M chainMonDom5Link.sql 2012-11-21 14:59 1.6K chainMonDom5Link.txt.gz 2012-11-21 15:01 1.3G chainPanTro4.sql 2012-11-21 14:53 1.7K chainPanTro4.txt.gz 2012-11-21 14:53 15M chainPanTro4Link.sql 2012-11-21 14:42 1.6K chainPanTro4Link.txt.gz 2012-11-21 14:42 165M chainPonAbe2.sql 2012-11-21 14:35 1.7K chainPonAbe2.txt.gz 2012-11-21 14:35 266M chainPonAbe2Link.sql 2012-11-21 14:36 1.6K chainPonAbe2Link.txt.gz 2012-11-21 14:37 817M chainRn5.sql 2012-11-21 14:34 1.7K chainRn5.txt.gz 2012-11-21 14:34 49M chainRn5Link.sql 2012-11-21 14:43 1.5K chainRn5Link.txt.gz 2012-11-21 14:43 447M chainTarSyr2.sql 2015-05-25 09:10 1.7K chainTarSyr2.txt.gz 2015-05-25 09:10 266M chainTarSyr2Link.sql 2015-05-25 09:11 1.5K chainTarSyr2Link.txt.gz 2015-05-25 09:12 1.1G chromInfo.sql 2012-11-21 15:09 1.4K chromInfo.txt.gz 2012-11-21 15:09 118K cpgIslandExt.sql 2012-11-21 15:08 1.7K cpgIslandExt.txt.gz 2012-11-21 15:08 546K cpgIslandExtUnmasked.sql 2014-06-01 19:17 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:17 1.1M ctgPos2.sql 2012-11-21 14:59 1.5K ctgPos2.txt.gz 2012-11-21 14:59 64K cytoBandIdeo.sql 2013-04-28 21:17 1.5K cytoBandIdeo.txt.gz 2013-04-28 21:17 113K estOrientInfo.sql 2012-11-21 15:09 1.8K estOrientInfo.txt.gz 2012-11-21 15:09 776K gap.sql 2012-11-21 14:58 1.6K gap.txt.gz 2012-11-21 14:58 5.2M gbLoaded.sql 2020-09-01 09:22 1.6K gbLoaded.txt.gz 2020-09-01 09:22 81K gc5BaseBw.sql 2012-11-21 14:50 1.3K gc5BaseBw.txt.gz 2012-11-21 14:50 63 geneid.sql 2015-11-22 21:02 1.9K geneid.txt.gz 2015-11-22 21:02 2.6M genscan.sql 2012-11-21 15:08 1.7K genscan.txt.gz 2012-11-21 15:08 2.8M gold.sql 2012-11-21 14:55 1.7K gold.txt.gz 2012-11-21 14:55 539K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-10-25 08:24 1.7K hgFindSpec.txt.gz 2020-10-25 08:24 729 history.sql 2012-11-21 15:08 1.6K history.txt.gz 2012-11-21 15:08 837 intronEst.sql 2012-11-21 15:10 2.1K intronEst.txt.gz 2012-11-21 15:10 2.1M microsat.sql 2015-08-24 00:53 1.5K microsat.txt.gz 2015-08-24 00:53 262K mrnaOrientInfo.sql 2020-09-01 09:22 1.8K mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M nestedRepeats.sql 2012-11-21 15:10 1.9K nestedRepeats.txt.gz 2012-11-21 15:10 17M netCalJac3.sql 2012-11-21 15:09 2.1K netCalJac3.txt.gz 2012-11-21 15:09 46M netGorGor3.sql 2012-11-21 14:53 2.1K netGorGor3.txt.gz 2012-11-21 14:53 36M netHg19.sql 2012-11-21 15:10 2.1K netHg19.txt.gz 2012-11-21 15:10 26M netHg38.sql 2015-05-18 07:55 2.1K netHg38.txt.gz 2015-05-18 07:55 26M netMm10.sql 2012-11-21 15:12 2.1K netMm10.txt.gz 2012-11-21 15:12 70M netMonDom5.sql 2012-11-21 14:58 2.1K netMonDom5.txt.gz 2012-11-21 14:58 18M netPanTro4.sql 2012-11-21 14:50 2.1K netPanTro4.txt.gz 2012-11-21 14:50 28M netPonAbe2.sql 2012-11-21 14:34 2.1K netPonAbe2.txt.gz 2012-11-21 14:34 36M netRn5.sql 2012-11-21 15:11 2.1K netRn5.txt.gz 2012-11-21 15:11 70M netTarSyr2.sql 2015-05-25 09:16 2.1K netTarSyr2.txt.gz 2015-05-25 09:16 69M refFlat.sql 2020-09-01 09:22 1.7K refFlat.txt.gz 2020-09-01 09:22 526K refGene.sql 2020-09-01 09:22 1.9K refGene.txt.gz 2020-09-01 09:22 571K refSeqAli.sql 2020-09-01 09:22 2.1K refSeqAli.txt.gz 2020-09-01 09:22 588K rmsk.sql 2012-11-21 15:07 1.9K rmsk.txt.gz 2012-11-21 15:07 134M simpleRepeat.sql 2012-11-21 15:09 1.9K simpleRepeat.txt.gz 2012-11-21 15:09 24M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 3.8K trackDb.sql 2020-10-22 20:43 2.0K trackDb.txt.gz 2020-10-22 20:43 32K ucscToINSDC.sql 2013-09-15 18:55 1.4K ucscToINSDC.txt.gz 2013-09-15 18:55 188K windowmaskerSdust.sql 2012-11-21 15:12 1.5K windowmaskerSdust.txt.gz 2012-11-21 15:12 145M xenoMrna.sql 2020-09-01 09:22 2.1K xenoMrna.txt.gz 2020-09-01 09:22 323M xenoRefFlat.sql 2020-09-01 09:22 1.7K xenoRefFlat.txt.gz 2020-09-01 09:22 29M xenoRefGene.sql 2020-09-01 09:22 1.9K xenoRefGene.txt.gz 2020-09-01 09:22 33M xenoRefSeqAli.sql 2020-09-01 09:22 2.1K xenoRefSeqAli.txt.gz 2020-09-01 09:22 34M