This directory contains a dump of the UCSC genome annotation database for the
Jun. 2017 (CHOK1S_HZDv1/criGriChoV2) assembly of the chinese hamster genome
(criGriChoV2, Eagle Genomics Ltd) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/2791
https://www.ncbi.nlm.nih.gov/genome/assembly/1422381
https://www.ncbi.nlm.nih.gov/bioproject/PRJEB21211
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=criGriChoV2
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.soe.ucsc.edu, then go to
the directory goldenPath/criGriChoV2/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.soe.ucsc.edu/goldenPath/criGriChoV2/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 criGriChoV2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql criGriChoV2 --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.
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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 -
bigFiles.txt.gz 2024-11-17 03:13 73
bigFiles.sql 2024-11-17 03:13 1.4K
tableList.txt.gz 2024-11-17 03:13 2.7K
tableList.sql 2024-11-17 03:13 1.6K
tableDescriptions.txt.gz 2024-11-16 02:04 5.6K
tableDescriptions.sql 2024-11-16 02:04 1.5K
hgFindSpec.txt.gz 2023-03-28 13:47 873
hgFindSpec.sql 2023-03-28 13:47 1.8K
trackDb.txt.gz 2023-03-28 13:47 43K
trackDb.sql 2023-03-28 13:47 2.1K
ensPep.txt.gz 2021-05-25 14:32 6.6M
ensPep.sql 2021-05-25 14:32 1.3K
ensemblSource.txt.gz 2021-05-25 14:32 87K
ensemblSource.sql 2021-05-25 14:32 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:27 167K
ensemblToGeneName.sql 2021-05-25 14:27 1.4K
ensGtp.txt.gz 2021-05-25 14:27 297K
ensGtp.sql 2021-05-25 14:27 1.4K
ensGene.txt.gz 2021-05-25 14:27 2.3M
ensGene.sql 2021-05-25 14:27 1.9K
xenoRefSeqAli.txt.gz 2019-06-05 10:43 29M
xenoRefSeqAli.sql 2019-06-05 10:43 2.1K
xenoRefGene.txt.gz 2019-06-05 10:43 32M
xenoRefGene.sql 2019-06-05 10:43 1.9K
xenoRefFlat.txt.gz 2019-06-05 10:43 29M
xenoRefFlat.sql 2019-06-05 10:43 1.7K
windowmaskerSdust.txt.gz 2019-06-05 10:43 123M
windowmaskerSdust.sql 2019-06-05 10:43 1.5K
ucscToRefSeq.txt.gz 2019-06-05 10:43 62
ucscToRefSeq.sql 2019-06-05 10:43 1.4K
ucscToINSDC.txt.gz 2019-06-05 10:43 50K
ucscToINSDC.sql 2019-06-05 10:43 1.4K
genscan.txt.gz 2019-06-05 10:43 3.2M
genscan.sql 2019-06-05 10:43 1.7K
gc5BaseBw.txt.gz 2019-06-05 10:43 70
gc5BaseBw.sql 2019-06-05 10:43 1.3K
gapOverlap.txt.gz 2019-06-05 10:43 232K
gapOverlap.sql 2019-06-05 10:43 1.8K
netHg38.txt.gz 2019-06-05 10:42 54M
netHg38.sql 2019-06-05 10:42 2.1K
estOrientInfo.txt.gz 2019-06-05 10:42 286
estOrientInfo.sql 2019-06-05 10:42 1.8K
nestedRepeats.txt.gz 2019-06-05 10:42 8.9M
nestedRepeats.sql 2019-06-05 10:42 1.9K
mrnaOrientInfo.txt.gz 2019-06-05 10:42 848K
mrnaOrientInfo.sql 2019-06-05 10:42 1.8K
tandemDups.txt.gz 2019-06-05 10:42 9.6M
tandemDups.sql 2019-06-05 10:42 1.8K
simpleRepeat.txt.gz 2019-06-05 10:42 23M
simpleRepeat.sql 2019-06-05 10:42 1.9K
microsat.txt.gz 2019-06-05 10:42 2.3M
microsat.sql 2019-06-05 10:42 1.5K
cytoBandIdeo.txt.gz 2019-06-05 10:42 31K
cytoBandIdeo.sql 2019-06-05 10:42 1.5K
intronEst.txt.gz 2019-06-05 10:42 560
intronEst.sql 2019-06-05 10:42 2.1K
gap.txt.gz 2019-06-05 10:42 728K
gap.sql 2019-06-05 10:42 1.6K
cpgIslandExtUnmasked.txt.gz 2019-06-05 10:42 420K
cpgIslandExtUnmasked.sql 2019-06-05 10:42 1.7K
cpgIslandExt.txt.gz 2019-06-05 10:42 410K
cpgIslandExt.sql 2019-06-05 10:42 1.7K
chromInfo.txt.gz 2019-06-05 10:42 33K
chromInfo.sql 2019-06-05 10:42 1.4K
rmsk.txt.gz 2019-06-05 10:42 107M
rmsk.sql 2019-06-05 10:41 1.9K
history.txt.gz 2019-06-05 10:41 823
history.sql 2019-06-05 10:41 1.6K
chromAlias.txt.gz 2019-06-05 10:41 80K
chromAlias.sql 2019-06-05 10:41 1.4K
chainMm10Link.txt.gz 2019-06-05 10:35 1.8G
chainMm10Link.sql 2019-06-05 10:32 1.5K
chainMm10.txt.gz 2019-06-05 10:31 412M
refSeqAli.txt.gz 2019-06-05 10:30 43K
refSeqAli.sql 2019-06-05 10:30 2.1K
grp.txt.gz 2019-06-05 10:30 213
grp.sql 2019-06-05 10:30 1.4K
chainMm10.sql 2019-06-05 10:30 1.7K
chainHg38Link.txt.gz 2019-06-05 10:25 1.4G
chainHg38Link.sql 2019-06-05 10:23 1.5K
chainHg38.txt.gz 2019-06-05 10:22 442M
chainHg38.sql 2019-06-05 10:21 1.7K
refGene.txt.gz 2019-06-05 10:21 43K
refGene.sql 2019-06-05 10:21 1.9K
gold.txt.gz 2019-06-05 10:21 1.2M
gold.sql 2019-06-05 10:21 1.7K
augustusGene.txt.gz 2019-06-05 10:21 2.3M
augustusGene.sql 2019-06-05 10:21 1.9K
refFlat.txt.gz 2019-06-05 10:21 39K
refFlat.sql 2019-06-05 10:21 1.7K
all_mrna.txt.gz 2019-06-05 10:21 2.8M
all_mrna.sql 2019-06-05 10:21 2.1K
all_est.txt.gz 2019-06-05 10:21 838
all_est.sql 2019-06-05 10:21 2.1K
netMm10.txt.gz 2019-06-05 10:21 80M
netMm10.sql 2019-06-05 10:21 2.1K