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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-18 16:24 35M
xenoRefSeqAli.sql 2020-08-18 16:24 2.1K
xenoRefGene.txt.gz 2020-08-18 16:24 33M
xenoRefGene.sql 2020-08-18 16:24 2.0K
xenoRefFlat.txt.gz 2020-08-18 16:24 30M
xenoRefFlat.sql 2020-08-18 16:24 1.7K
windowmaskerSdust.txt.gz 2013-01-24 15:54 135M
windowmaskerSdust.sql 2013-01-24 15:54 1.5K
ucscToRefSeq.txt.gz 2018-02-18 05:47 23K
ucscToRefSeq.sql 2018-02-18 05:47 1.4K
ucscToINSDC.txt.gz 2013-09-15 10:13 22K
ucscToINSDC.sql 2013-09-15 10:13 1.4K
trackDb.txt.gz 2024-01-31 15:13 45K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-17 03:38 3.0K
tableList.sql 2024-11-17 03:38 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
simpleRepeat.txt.gz 2013-01-24 15:39 11M
simpleRepeat.sql 2013-01-24 15:39 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 558K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
rmsk.txt.gz 2013-01-24 15:39 96M
rmsk.sql 2013-01-24 15:39 1.9K
netMonDom5.txt.gz 2013-01-24 15:40 25M
netMonDom5.sql 2013-01-24 15:40 2.1K
netMm10.txt.gz 2013-01-24 15:55 70M
netMm10.sql 2013-01-24 15:55 2.1K
netHg19.txt.gz 2013-01-24 15:52 54M
netHg19.sql 2013-01-24 15:52 2.1K
netBosTau7.txt.gz 2013-01-24 15:38 64M
netBosTau7.sql 2013-01-24 15:38 2.1K
nestedRepeats.txt.gz 2013-01-24 15:55 11M
nestedRepeats.sql 2013-01-24 15:55 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.0M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.5M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.1M
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.1M
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 226K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.5M
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
mrnaOrientInfo.txt.gz 2016-09-18 07:26 864
mrnaOrientInfo.sql 2016-09-18 07:26 1.8K
microsat.txt.gz 2015-08-23 12:21 175K
microsat.sql 2015-08-23 12:21 1.5K
history.txt.gz 2013-01-24 15:44 507
history.sql 2013-01-24 15:44 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2014-03-02 03:40 208
grp.sql 2014-03-02 03:40 1.3K
gold.txt.gz 2013-01-24 15:53 1.0M
gold.sql 2013-01-24 15:53 1.7K
genscanSubopt.txt.gz 2013-01-24 15:46 6.2M
genscanSubopt.sql 2013-01-24 15:46 1.6K
genscan.txt.gz 2013-01-24 15:44 3.1M
genscan.sql 2013-01-24 15:44 1.7K
gc5BaseBw.txt.gz 2013-01-24 15:40 63
gc5BaseBw.sql 2013-01-24 15:40 1.3K
gbLoaded.txt.gz 2020-08-18 16:24 31K
gbLoaded.sql 2020-08-18 16:24 1.6K
gap.txt.gz 2013-01-24 15:54 765K
gap.sql 2013-01-24 15:54 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 90
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
cytoBandIdeo.txt.gz 2013-04-28 12:00 15K
cytoBandIdeo.sql 2013-04-28 12:00 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 10:08 780K
cpgIslandExtUnmasked.sql 2014-06-01 10:08 1.7K
cpgIslandExt.txt.gz 2013-01-24 15:38 734K
cpgIslandExt.sql 2013-01-24 15:38 1.7K
chromInfo.txt.gz 2013-01-24 15:53 15K
chromInfo.sql 2013-01-24 15:53 1.4K
chromAlias.txt.gz 2018-02-18 05:47 30K
chromAlias.sql 2018-02-18 05:47 1.4K
chainMonDom5Link.txt.gz 2013-01-24 15:48 1.0G
chainMonDom5Link.sql 2013-01-24 15:46 1.6K
chainMonDom5.txt.gz 2013-01-24 15:53 249M
chainMonDom5.sql 2013-01-24 15:52 1.7K
chainMm10Link.txt.gz 2013-01-24 15:42 647M
chainMm10Link.sql 2013-01-24 15:41 1.5K
chainMm10.txt.gz 2013-01-24 15:22 111M
chainMm10.sql 2013-01-24 15:21 1.7K
chainHg19Link.txt.gz 2013-01-24 15:24 1.0G
chainHg19Link.sql 2013-01-24 15:22 1.5K
chainHg19.txt.gz 2013-01-24 15:40 265M
chainHg19.sql 2013-01-24 15:39 1.7K
chainBosTau7Link.txt.gz 2013-01-24 15:32 1.7G
chainBosTau7Link.sql 2013-01-24 15:29 1.6K
chainBosTau7.txt.gz 2013-01-24 15:45 383M
chainBosTau7.sql 2013-01-24 15:44 1.7K
bigFiles.txt.gz 2024-11-17 03:38 94
bigFiles.sql 2024-11-17 03:38 1.4K
augustusGene.txt.gz 2015-07-26 11:24 2.6M
augustusGene.sql 2015-07-26 11:24 1.9K
all_mrna.txt.gz 2016-09-18 07:26 2.9K
all_mrna.sql 2016-09-18 07:26 2.1K