This directory contains a dump of the UCSC genome annotation database for the
    Nov. 2015 (BCM Mmul_8.0.1/rheMac8) assembly of the rhesus genome
    (rheMac8, Baylor College of Medicine Genome Sequencing Center) .

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/2715158
    http://www.ncbi.nlm.nih.gov/bioproject/12537

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=rheMac8
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/rheMac8/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/rheMac8/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/rheMac8/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 rheMac8 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac8 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

For conditions of use regarding the Rhesus genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use

-----------------------------------------------------------------------------
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 2016-04-12 13:20 2.1K all_est.txt.gz 2016-04-12 13:20 3.4M all_mrna.sql 2020-09-01 09:22 2.1K all_mrna.txt.gz 2020-09-01 09:22 16M augustusGene.sql 2016-04-12 13:20 1.9K augustusGene.txt.gz 2016-04-12 13:20 2.3M bigFiles.sql 2021-05-09 03:03 1.4K bigFiles.txt.gz 2021-05-09 03:03 69 chainChlSab2.sql 2016-10-30 09:48 1.7K chainChlSab2.txt.gz 2016-10-30 09:48 23M chainChlSab2Link.sql 2016-10-30 09:48 1.5K chainChlSab2Link.txt.gz 2016-10-30 09:48 122M chainHg38.sql 2016-04-12 13:20 1.7K chainHg38.txt.gz 2016-04-12 13:20 25M chainHg38Link.sql 2016-04-12 13:20 1.5K chainHg38Link.txt.gz 2016-04-12 13:21 211M chainMm10.sql 2016-04-12 13:21 1.7K chainMm10.txt.gz 2016-04-12 13:21 71M chainMm10Link.sql 2016-04-12 13:22 1.5K chainMm10Link.txt.gz 2016-04-12 13:22 515M chainRn6.sql 2017-03-28 02:24 1.7K chainRn6.txt.gz 2017-03-28 02:31 615M chainRn6Link.sql 2017-03-28 02:53 1.5K chainRn6Link.txt.gz 2017-03-28 03:19 2.3G chromAlias.sql 2018-02-18 08:25 1.4K chromAlias.txt.gz 2018-02-18 08:25 2.9M chromInfo.sql 2016-04-12 13:25 1.4K chromInfo.txt.gz 2016-04-12 13:25 1.3M cpgIslandExt.sql 2016-04-12 13:25 1.7K cpgIslandExt.txt.gz 2016-04-12 13:25 675K cpgIslandExtUnmasked.sql 2016-04-12 13:26 1.7K cpgIslandExtUnmasked.txt.gz 2016-04-12 13:26 1.8M cytoBandIdeo.sql 2016-04-12 13:26 1.5K cytoBandIdeo.txt.gz 2016-04-12 13:26 1.4M ensGene.sql 2019-02-10 03:42 1.9K ensGene.txt.gz 2019-02-10 03:42 3.3M ensGtp.sql 2019-02-10 03:42 1.4K ensGtp.txt.gz 2019-02-10 03:42 591K ensPep.sql 2019-02-10 03:42 1.3K ensPep.txt.gz 2019-02-10 03:42 12M ensemblSource.sql 2019-02-10 03:42 1.4K ensemblSource.txt.gz 2019-02-10 03:42 170K ensemblToGeneName.sql 2019-02-10 03:42 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:42 284K estOrientInfo.sql 2016-04-12 13:26 1.8K estOrientInfo.txt.gz 2016-04-12 13:26 791K gap.sql 2016-04-12 13:26 1.6K gap.txt.gz 2016-04-12 13:26 810K gbLoaded.sql 2020-09-01 09:22 1.6K gbLoaded.txt.gz 2020-09-01 09:22 44K gc5BaseBw.sql 2016-04-12 13:25 1.3K gc5BaseBw.txt.gz 2016-04-12 13:25 66 genscan.sql 2016-04-12 13:26 1.7K genscan.txt.gz 2016-04-12 13:26 3.0M gold.sql 2016-04-12 13:26 1.7K gold.txt.gz 2016-04-12 13:26 3.9M grp.sql 2016-04-12 13:26 1.3K grp.txt.gz 2016-04-12 13:26 213 hgFindSpec.sql 2021-01-21 09:36 1.8K hgFindSpec.txt.gz 2021-01-21 09:36 816 history.sql 2016-04-12 13:20 1.6K history.txt.gz 2016-04-12 13:20 513 intronEst.sql 2016-04-12 13:20 2.1K intronEst.txt.gz 2016-04-12 13:20 2.2M microsat.sql 2016-04-12 13:21 1.5K microsat.txt.gz 2016-04-12 13:21 399K mrnaOrientInfo.sql 2020-09-01 09:22 1.8K mrnaOrientInfo.txt.gz 2020-09-01 09:22 4.2M nestedRepeats.sql 2016-04-12 13:26 1.9K nestedRepeats.txt.gz 2016-04-12 13:26 18M netChlSab2.sql 2016-10-30 09:48 2.1K netChlSab2.txt.gz 2016-10-30 09:48 17M netHg38.sql 2016-04-12 13:28 2.1K netHg38.txt.gz 2016-04-12 13:28 26M netMm10.sql 2016-04-12 13:29 2.1K netMm10.txt.gz 2016-04-12 13:29 72M netRn6.sql 2017-03-28 04:41 2.1K netRn6.txt.gz 2017-03-28 04:42 79M 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 566K refSeqAli.sql 2020-09-01 09:22 2.1K refSeqAli.txt.gz 2020-09-01 09:22 574K rmsk.sql 2016-04-12 13:30 1.9K rmsk.txt.gz 2016-04-12 13:30 150M simpleRepeat.sql 2016-04-12 13:30 1.9K simpleRepeat.txt.gz 2016-04-12 13:30 42M tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 6.9K tableList.sql 2021-05-09 03:03 1.6K tableList.txt.gz 2021-05-09 03:03 3.0K trackDb.sql 2021-01-21 09:36 2.1K trackDb.txt.gz 2021-01-21 09:36 41K ucscToINSDC.sql 2016-04-12 13:31 1.4K ucscToINSDC.txt.gz 2016-04-12 13:31 2.1M ucscToRefSeq.sql 2018-02-18 08:25 1.4K ucscToRefSeq.txt.gz 2018-02-18 08:25 2.1M windowmaskerSdust.sql 2016-04-12 13:31 1.5K windowmaskerSdust.txt.gz 2016-04-12 13:31 151M xenoRefFlat.sql 2020-09-01 09:22 1.7K xenoRefFlat.txt.gz 2020-09-01 09:22 24M xenoRefGene.sql 2020-09-01 09:22 1.9K xenoRefGene.txt.gz 2020-09-01 09:22 26M xenoRefSeqAli.sql 2020-09-01 09:22 2.1K xenoRefSeqAli.txt.gz 2020-09-01 09:22 26M