This directory contains a dump of the UCSC genome annotation database for
the May 2012 (CerSimSim1.0/cerSim1) assembly of the white rhinoceros genome (cerSim1, Broad Institute).
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/11839
http://www.ncbi.nlm.nih.gov/genome/assembly/406328
http://www.ncbi.nlm.nih.gov/bioproject/74583
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=cerSim1
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/cerSim1/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/cerSim1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/cerSim1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/cerSim1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/cerSim1/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 cerSim1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql cerSim1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The White rhinoceros sequence is made freely available before scientific publication
with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
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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 -
chainMm10.sql 2013-01-24 15:21 1.7K
chainMm10.txt.gz 2013-01-24 15:22 111M
chainHg19Link.sql 2013-01-24 15:22 1.5K
chainHg19Link.txt.gz 2013-01-24 15:24 1.0G
chainBosTau7Link.sql 2013-01-24 15:29 1.6K
chainBosTau7Link.txt.gz 2013-01-24 15:32 1.7G
cpgIslandExt.sql 2013-01-24 15:38 1.7K
cpgIslandExt.txt.gz 2013-01-24 15:38 734K
netBosTau7.sql 2013-01-24 15:38 2.1K
netBosTau7.txt.gz 2013-01-24 15:38 64M
rmsk.sql 2013-01-24 15:39 1.9K
rmsk.txt.gz 2013-01-24 15:39 96M
simpleRepeat.sql 2013-01-24 15:39 1.9K
simpleRepeat.txt.gz 2013-01-24 15:39 11M
chainHg19.sql 2013-01-24 15:39 1.7K
chainHg19.txt.gz 2013-01-24 15:40 265M
gc5BaseBw.sql 2013-01-24 15:40 1.3K
gc5BaseBw.txt.gz 2013-01-24 15:40 63
netMonDom5.sql 2013-01-24 15:40 2.1K
netMonDom5.txt.gz 2013-01-24 15:40 25M
chainMm10Link.sql 2013-01-24 15:41 1.5K
chainMm10Link.txt.gz 2013-01-24 15:42 647M
genscan.sql 2013-01-24 15:44 1.7K
genscan.txt.gz 2013-01-24 15:44 3.1M
history.sql 2013-01-24 15:44 1.6K
history.txt.gz 2013-01-24 15:44 507
chainBosTau7.sql 2013-01-24 15:44 1.7K
chainBosTau7.txt.gz 2013-01-24 15:45 383M
genscanSubopt.sql 2013-01-24 15:46 1.6K
genscanSubopt.txt.gz 2013-01-24 15:46 6.2M
chainMonDom5Link.sql 2013-01-24 15:46 1.6K
chainMonDom5Link.txt.gz 2013-01-24 15:48 1.0G
netHg19.sql 2013-01-24 15:52 2.1K
netHg19.txt.gz 2013-01-24 15:52 54M
chainMonDom5.sql 2013-01-24 15:52 1.7K
chainMonDom5.txt.gz 2013-01-24 15:53 249M
chromInfo.sql 2013-01-24 15:53 1.4K
chromInfo.txt.gz 2013-01-24 15:53 15K
gold.sql 2013-01-24 15:53 1.7K
gold.txt.gz 2013-01-24 15:53 1.0M
gap.sql 2013-01-24 15:54 1.6K
gap.txt.gz 2013-01-24 15:54 765K
windowmaskerSdust.sql 2013-01-24 15:54 1.5K
windowmaskerSdust.txt.gz 2013-01-24 15:54 135M
netMm10.sql 2013-01-24 15:55 2.1K
netMm10.txt.gz 2013-01-24 15:55 70M
nestedRepeats.sql 2013-01-24 15:55 1.9K
nestedRepeats.txt.gz 2013-01-24 15:55 11M
cytoBandIdeo.sql 2013-04-28 12:00 1.5K
cytoBandIdeo.txt.gz 2013-04-28 12:00 15K
ucscToINSDC.sql 2013-09-15 10:13 1.4K
ucscToINSDC.txt.gz 2013-09-15 10:13 22K
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 208
cpgIslandExtUnmasked.sql 2014-06-01 10:08 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:08 780K
augustusGene.sql 2015-07-26 11:24 1.9K
augustusGene.txt.gz 2015-07-26 11:24 2.6M
microsat.sql 2015-08-23 12:21 1.5K
microsat.txt.gz 2015-08-23 12:21 175K
mrnaOrientInfo.sql 2016-09-18 07:26 1.8K
mrnaOrientInfo.txt.gz 2016-09-18 07:26 864
all_mrna.sql 2016-09-18 07:26 2.1K
all_mrna.txt.gz 2016-09-18 07:26 2.9K
chromAlias.sql 2018-02-18 05:47 1.4K
chromAlias.txt.gz 2018-02-18 05:47 30K
ucscToRefSeq.sql 2018-02-18 05:47 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:47 23K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 90
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.5M
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 226K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.1M
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.1M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.5M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.0M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 558K
xenoRefGene.sql 2020-08-18 16:24 2.0K
xenoRefGene.txt.gz 2020-08-18 16:24 33M
xenoRefFlat.sql 2020-08-18 16:24 1.7K
xenoRefFlat.txt.gz 2020-08-18 16:24 30M
xenoRefSeqAli.sql 2020-08-18 16:24 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 16:24 35M
gbLoaded.sql 2020-08-18 16:24 1.6K
gbLoaded.txt.gz 2020-08-18 16:24 31K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 30K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 45K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.2K
tableList.sql 2024-04-14 03:35 1.6K
tableList.txt.gz 2024-04-14 03:35 3.1K
bigFiles.sql 2024-04-14 03:35 1.4K
bigFiles.txt.gz 2024-04-14 03:35 94