This directory contains a dump of the UCSC genome annotation database for the
Jul. 2013 (C_griseus_v1.0/criGri1) assembly of the chinese hamster genome
(criGri1, Beijing Genomics Institution-Shenzhen) .
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/2791
http://www.ncbi.nlm.nih.gov/genome/assembly/40911
http://www.ncbi.nlm.nih.gov/bioproject/167053
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=criGri1
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/criGri1/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/criGri1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/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 criGri1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql criGri1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 -
xenoRefSeqAli.txt.gz 2020-08-18 20:53 44M
xenoRefSeqAli.sql 2020-08-18 20:53 2.1K
xenoRefGene.txt.gz 2020-08-18 20:40 42M
xenoRefGene.sql 2020-08-18 20:40 2.0K
xenoRefFlat.txt.gz 2020-08-18 20:53 38M
xenoRefFlat.sql 2020-08-18 20:53 1.7K
xenoMrna.txt.gz 2018-07-29 05:38 33
xenoMrna.sql 2018-07-29 05:38 2.1K
windowmaskerSdust.txt.gz 2014-05-08 12:04 84M
windowmaskerSdust.sql 2014-05-08 12:03 1.5K
ucscToINSDC.txt.gz 2014-05-08 12:03 307K
ucscToINSDC.sql 2014-05-08 12:03 1.4K
trackDb_pushedout.txt.gz 2021-08-02 14:27 37K
trackDb_pushedout.sql 2021-08-02 14:27 2.1K
trackDb.txt.gz 2023-03-28 13:47 39K
trackDb.sql 2023-03-28 13:47 2.1K
tableList.txt.gz 2024-04-21 03:38 2.8K
tableList.sql 2024-04-21 03:38 1.6K
tableDescriptions.txt.gz 2024-04-20 02:03 5.3K
tableDescriptions.sql 2024-04-20 02:03 1.5K
simpleRepeat.txt.gz 2014-05-08 12:03 23M
simpleRepeat.sql 2014-05-08 12:03 1.9K
rmsk.txt.gz 2014-05-08 12:03 101M
rmsk.sql 2014-05-08 12:03 1.9K
refSeqAli.txt.gz 2020-05-06 06:20 44K
refSeqAli.sql 2020-05-06 06:20 2.1K
refGene.txt.gz 2020-08-18 20:36 39K
refGene.sql 2020-08-18 20:36 1.9K
refFlat.txt.gz 2020-08-18 20:36 36K
refFlat.sql 2020-08-18 20:36 1.7K
netHg19.txt.gz 2014-05-08 12:02 51M
netHg19.sql 2014-05-08 12:02 2.1K
netCriGriChoV1.txt.gz 2017-11-26 06:38 16M
netCriGriChoV1.sql 2017-11-26 06:38 2.1K
nestedRepeats.txt.gz 2014-05-08 11:57 8.9M
nestedRepeats.sql 2014-05-08 11:57 1.9K
mrnaOrientInfo.txt.gz 2020-05-06 06:16 802K
mrnaOrientInfo.sql 2020-05-06 06:16 1.8K
microsat.txt.gz 2015-08-23 12:50 2.0M
microsat.sql 2015-08-23 12:50 1.5K
locusName.txt.gz 2017-08-20 09:02 9.1M
locusName.sql 2017-08-20 09:02 1.5K
intronEst.txt.gz 2014-05-08 11:56 533
intronEst.sql 2014-05-08 11:56 2.1K
history.txt.gz 2014-05-08 12:03 466
history.sql 2014-05-08 12:03 1.6K
hgFindSpec_pushedout.txt.gz 2021-08-02 14:27 660
hgFindSpec_pushedout.sql 2021-08-02 14:27 1.8K
hgFindSpec.txt.gz 2023-03-28 13:47 697
hgFindSpec.sql 2023-03-28 13:47 1.8K
grp.txt.gz 2014-05-08 12:03 206
grp.sql 2014-05-08 12:03 1.3K
gold.txt.gz 2014-05-08 12:03 3.0M
gold.sql 2014-05-08 12:03 1.7K
genscan.txt.gz 2014-05-08 12:03 3.0M
genscan.sql 2014-05-08 12:03 1.7K
gc5BaseBw.txt.gz 2014-05-08 12:03 66
gc5BaseBw.sql 2014-05-08 12:03 1.3K
gbLoaded.txt.gz 2020-08-18 20:53 65K
gbLoaded.sql 2020-08-18 20:53 1.6K
gap.txt.gz 2014-05-08 12:03 2.0M
gap.sql 2014-05-08 12:03 1.6K
estOrientInfo.txt.gz 2014-05-08 12:03 278
estOrientInfo.sql 2014-05-08 12:03 1.8K
cytoBandIdeo.txt.gz 2014-05-08 12:03 185K
cytoBandIdeo.sql 2014-05-08 12:03 1.5K
crisprTargets.txt.gz 2017-08-20 09:02 61
crisprTargets.sql 2017-08-20 09:02 1.3K
crisprRanges.txt.gz 2017-08-20 09:02 2.1M
crisprRanges.sql 2017-08-20 09:02 1.4K
cpgIslandExtUnmasked.txt.gz 2014-05-08 12:03 309K
cpgIslandExtUnmasked.sql 2014-05-08 12:03 1.7K
cpgIslandExt.txt.gz 2014-05-08 12:03 290K
cpgIslandExt.sql 2014-05-08 12:03 1.7K
chromInfo.txt.gz 2014-05-08 12:02 200K
chromInfo.sql 2014-05-08 12:02 1.4K
chainHg19Link.txt.gz 2014-05-08 11:59 1.0G
chainHg19Link.sql 2014-05-08 11:57 1.5K
chainHg19.txt.gz 2014-05-08 11:56 266M
chainHg19.sql 2014-05-08 11:56 1.7K
chainCriGriChoV1Link.txt.gz 2017-11-26 06:25 3.5G
chainCriGriChoV1Link.sql 2017-11-26 06:20 1.6K
chainCriGriChoV1.txt.gz 2017-11-26 06:18 788M
chainCriGriChoV1.sql 2017-11-26 06:17 1.7K
bigFiles.txt.gz 2024-04-21 03:38 92
bigFiles.sql 2024-04-21 03:38 1.4K
augustusGene.txt.gz 2015-07-26 11:46 2.1M
augustusGene.sql 2015-07-26 11:46 1.9K
all_mrna.txt.gz 2018-11-04 06:14 2.9M
all_mrna.sql 2018-11-04 06:14 2.1K
all_est.txt.gz 2014-05-08 11:56 790
all_est.sql 2014-05-08 11:56 2.1K