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 - gc5BaseBw.txt.gz 2012-11-21 14:50 63 bigFiles.txt.gz 2024-11-10 03:30 68 grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.txt.gz 2023-03-28 13:52 778 history.txt.gz 2012-11-21 15:08 837 gc5BaseBw.sql 2012-11-21 14:50 1.3K grp.sql 2014-03-02 04:14 1.3K chromInfo.sql 2012-11-21 15:09 1.4K bigFiles.sql 2024-11-10 03:30 1.4K ucscToINSDC.sql 2013-09-15 18:55 1.4K tableDescriptions.sql 2024-11-09 02:03 1.5K microsat.sql 2015-08-24 00:53 1.5K windowmaskerSdust.sql 2012-11-21 15:12 1.5K cytoBandIdeo.sql 2013-04-28 21:17 1.5K chainRn5Link.sql 2012-11-21 14:43 1.5K chainHg38Link.sql 2015-05-18 07:55 1.5K ctgPos2.sql 2012-11-21 14:59 1.5K chainHg19Link.sql 2012-11-21 14:58 1.5K chainMm10Link.sql 2012-11-21 14:47 1.5K chainTarSyr2Link.sql 2015-05-25 09:11 1.5K chainCalJac3Link.sql 2012-11-21 14:53 1.6K chainGorGor3Link.sql 2012-11-21 14:50 1.6K chainMonDom5Link.sql 2012-11-21 14:59 1.6K chainPanTro4Link.sql 2012-11-21 14:42 1.6K chainPonAbe2Link.sql 2012-11-21 14:36 1.6K history.sql 2012-11-21 15:08 1.6K tableList.sql 2024-11-10 03:30 1.6K gap.sql 2012-11-21 14:58 1.6K gbLoaded.sql 2020-09-01 09:22 1.6K gold.sql 2012-11-21 14:55 1.7K genscan.sql 2012-11-21 15:08 1.7K cpgIslandExt.sql 2012-11-21 15:08 1.7K chainRn5.sql 2012-11-21 14:34 1.7K chainHg38.sql 2015-05-18 07:56 1.7K chainHg19.sql 2012-11-21 15:07 1.7K chainMm10.sql 2012-11-21 14:45 1.7K chainTarSyr2.sql 2015-05-25 09:10 1.7K cpgIslandExtUnmasked.sql 2014-06-01 19:17 1.7K chainCalJac3.sql 2012-11-21 15:09 1.7K chainGorGor3.sql 2012-11-21 14:54 1.7K chainMonDom5.sql 2012-11-21 14:55 1.7K chainPanTro4.sql 2012-11-21 14:53 1.7K chainPonAbe2.sql 2012-11-21 14:35 1.7K refFlat.sql 2020-09-01 09:22 1.7K xenoRefFlat.sql 2020-09-01 09:22 1.7K hgFindSpec.sql 2023-03-28 13:52 1.8K estOrientInfo.sql 2012-11-21 15:09 1.8K mrnaOrientInfo.sql 2020-09-01 09:22 1.8K rmsk.sql 2012-11-21 15:07 1.9K geneid.sql 2015-11-22 21:02 1.9K simpleRepeat.sql 2012-11-21 15:09 1.9K nestedRepeats.sql 2012-11-21 15:10 1.9K augustusGene.sql 2015-07-26 17:21 1.9K refGene.sql 2020-09-01 09:22 1.9K xenoRefGene.sql 2020-09-01 09:22 2.0K trackDb.sql 2023-03-28 13:52 2.1K netRn5.sql 2012-11-21 15:11 2.1K netHg38.sql 2015-05-18 07:55 2.1K netHg19.sql 2012-11-21 15:10 2.1K netMm10.sql 2012-11-21 15:12 2.1K netTarSyr2.sql 2015-05-25 09:16 2.1K netCalJac3.sql 2012-11-21 15:09 2.1K netGorGor3.sql 2012-11-21 14:53 2.1K netMonDom5.sql 2012-11-21 14:58 2.1K netPanTro4.sql 2012-11-21 14:50 2.1K netPonAbe2.sql 2012-11-21 14:34 2.1K all_est.sql 2012-11-21 14:34 2.1K intronEst.sql 2012-11-21 15:10 2.1K all_mrna.sql 2020-09-01 09:22 2.1K xenoMrna.sql 2020-09-01 09:22 2.1K refSeqAli.sql 2020-09-01 09:22 2.1K xenoRefSeqAli.sql 2020-09-01 09:22 2.1K tableList.txt.gz 2024-11-10 03:30 3.9K tableDescriptions.txt.gz 2024-11-09 02:03 5.5K trackDb.txt.gz 2023-03-28 13:52 34K ctgPos2.txt.gz 2012-11-21 14:59 64K gbLoaded.txt.gz 2020-09-01 09:22 81K cytoBandIdeo.txt.gz 2013-04-28 21:17 113K chromInfo.txt.gz 2012-11-21 15:09 118K ucscToINSDC.txt.gz 2013-09-15 18:55 188K microsat.txt.gz 2015-08-24 00:53 262K refFlat.txt.gz 2020-09-01 09:22 526K gold.txt.gz 2012-11-21 14:55 539K cpgIslandExt.txt.gz 2012-11-21 15:08 546K refGene.txt.gz 2020-09-01 09:22 571K refSeqAli.txt.gz 2020-09-01 09:22 588K estOrientInfo.txt.gz 2012-11-21 15:09 776K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:17 1.1M intronEst.txt.gz 2012-11-21 15:10 2.1M augustusGene.txt.gz 2015-07-26 17:21 2.1M geneid.txt.gz 2015-11-22 21:02 2.6M genscan.txt.gz 2012-11-21 15:08 2.8M all_est.txt.gz 2012-11-21 14:34 3.5M mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M gap.txt.gz 2012-11-21 14:58 5.2M chainCalJac3.txt.gz 2012-11-21 15:09 13M chainHg19.txt.gz 2012-11-21 15:07 15M chainPanTro4.txt.gz 2012-11-21 14:53 15M all_mrna.txt.gz 2020-09-01 09:22 16M chainHg38.txt.gz 2015-05-18 07:56 16M nestedRepeats.txt.gz 2012-11-21 15:10 17M netMonDom5.txt.gz 2012-11-21 14:58 18M simpleRepeat.txt.gz 2012-11-21 15:09 24M netHg38.txt.gz 2015-05-18 07:55 26M netHg19.txt.gz 2012-11-21 15:10 26M netPanTro4.txt.gz 2012-11-21 14:50 28M xenoRefFlat.txt.gz 2020-09-01 09:22 29M xenoRefGene.txt.gz 2020-09-01 09:22 33M xenoRefSeqAli.txt.gz 2020-09-01 09:22 34M netPonAbe2.txt.gz 2012-11-21 14:34 36M netGorGor3.txt.gz 2012-11-21 14:53 36M netCalJac3.txt.gz 2012-11-21 15:09 46M chainRn5.txt.gz 2012-11-21 14:34 49M chainMm10.txt.gz 2012-11-21 14:45 60M netTarSyr2.txt.gz 2015-05-25 09:16 69M netRn5.txt.gz 2012-11-21 15:11 70M netMm10.txt.gz 2012-11-21 15:12 70M rmsk.txt.gz 2012-11-21 15:07 134M windowmaskerSdust.txt.gz 2012-11-21 15:12 145M chainPanTro4Link.txt.gz 2012-11-21 14:42 165M chainHg19Link.txt.gz 2012-11-21 14:58 168M chainHg38Link.txt.gz 2015-05-18 07:55 176M chainGorGor3.txt.gz 2012-11-21 14:55 218M chainCalJac3Link.txt.gz 2012-11-21 14:53 221M chainPonAbe2.txt.gz 2012-11-21 14:35 266M chainTarSyr2.txt.gz 2015-05-25 09:10 266M xenoMrna.txt.gz 2020-09-01 09:22 323M chainRn5Link.txt.gz 2012-11-21 14:43 447M chainMm10Link.txt.gz 2012-11-21 14:48 474M chainMonDom5.txt.gz 2012-11-21 14:56 539M chainGorGor3Link.txt.gz 2012-11-21 14:51 646M chainPonAbe2Link.txt.gz 2012-11-21 14:37 817M chainTarSyr2Link.txt.gz 2015-05-25 09:12 1.1G chainMonDom5Link.txt.gz 2012-11-21 15:01 1.3G