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.
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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 -
all_est.sql 08-May-2014 11:56 2.1K
all_est.txt.gz 08-May-2014 11:56 790
all_mrna.sql 01-Jan-2017 11:27 2.1K
all_mrna.txt.gz 01-Jan-2017 11:27 2.9M
augustusGene.sql 26-Jul-2015 11:46 1.9K
augustusGene.txt.gz 26-Jul-2015 11:46 2.1M
bigFiles.sql 09-Jul-2017 08:24 1.4K
bigFiles.txt.gz 09-Jul-2017 08:24 69
chainHg19.sql 08-May-2014 11:56 1.7K
chainHg19.txt.gz 08-May-2014 11:56 266M
chainHg19Link.sql 08-May-2014 11:57 1.5K
chainHg19Link.txt.gz 08-May-2014 11:59 1.0G
chromInfo.sql 08-May-2014 12:02 1.4K
chromInfo.txt.gz 08-May-2014 12:02 200K
cpgIslandExt.sql 08-May-2014 12:03 1.7K
cpgIslandExt.txt.gz 08-May-2014 12:03 290K
cpgIslandExtUnmasked.sql 08-May-2014 12:03 1.7K
cpgIslandExtUnmasked.txt.gz 08-May-2014 12:03 309K
cytoBandIdeo.sql 08-May-2014 12:03 1.5K
cytoBandIdeo.txt.gz 08-May-2014 12:03 185K
estOrientInfo.sql 08-May-2014 12:03 1.8K
estOrientInfo.txt.gz 08-May-2014 12:03 278
gap.sql 08-May-2014 12:03 1.6K
gap.txt.gz 08-May-2014 12:03 2.0M
gbLoaded.sql 09-Jul-2017 08:24 1.6K
gbLoaded.txt.gz 09-Jul-2017 08:24 37K
gc5BaseBw.sql 08-May-2014 12:03 1.3K
gc5BaseBw.txt.gz 08-May-2014 12:03 66
genscan.sql 08-May-2014 12:03 1.7K
genscan.txt.gz 08-May-2014 12:03 3.0M
gold.sql 08-May-2014 12:03 1.7K
gold.txt.gz 08-May-2014 12:03 3.0M
grp.sql 08-May-2014 12:03 1.3K
grp.txt.gz 08-May-2014 12:03 206
hgFindSpec.sql 09-Jul-2017 08:24 1.7K
hgFindSpec.txt.gz 09-Jul-2017 08:24 578
history.sql 08-May-2014 12:03 1.6K
history.txt.gz 08-May-2014 12:03 466
intronEst.sql 08-May-2014 11:56 2.1K
intronEst.txt.gz 08-May-2014 11:56 533
microsat.sql 23-Aug-2015 12:50 1.5K
microsat.txt.gz 23-Aug-2015 12:50 2.0M
mrnaOrientInfo.sql 09-Jul-2017 08:24 1.8K
mrnaOrientInfo.txt.gz 09-Jul-2017 08:24 801K
nestedRepeats.sql 08-May-2014 11:57 1.9K
nestedRepeats.txt.gz 08-May-2014 11:57 8.9M
netHg19.sql 08-May-2014 12:02 2.1K
netHg19.txt.gz 08-May-2014 12:02 51M
refFlat.sql 09-Jul-2017 08:24 1.7K
refFlat.txt.gz 09-Jul-2017 08:24 35K
refGene.sql 09-Jul-2017 08:24 1.9K
refGene.txt.gz 09-Jul-2017 08:24 39K
refSeqAli.sql 18-Sep-2016 07:34 2.1K
refSeqAli.txt.gz 18-Sep-2016 07:34 43K
rmsk.sql 08-May-2014 12:03 1.9K
rmsk.txt.gz 08-May-2014 12:03 101M
simpleRepeat.sql 08-May-2014 12:03 1.9K
simpleRepeat.txt.gz 08-May-2014 12:03 23M
tableDescriptions.sql 09-Jul-2017 08:24 1.4K
tableDescriptions.txt.gz 09-Jul-2017 08:24 4.2K
tableList.sql 09-Jul-2017 08:24 1.5K
tableList.txt.gz 09-Jul-2017 08:24 2.4K
trackDb.sql 09-Jul-2017 08:24 2.0K
trackDb.txt.gz 09-Jul-2017 08:24 27K
ucscToINSDC.sql 08-May-2014 12:03 1.4K
ucscToINSDC.txt.gz 08-May-2014 12:03 307K
windowmaskerSdust.sql 08-May-2014 12:03 1.5K
windowmaskerSdust.txt.gz 08-May-2014 12:04 84M
xenoMrna.sql 09-Jul-2017 08:24 2.1K
xenoMrna.txt.gz 09-Jul-2017 08:24 33
xenoRefFlat.sql 09-Jul-2017 08:24 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 08:24 33M
xenoRefGene.sql 09-Jul-2017 08:24 1.9K
xenoRefGene.txt.gz 09-Jul-2017 08:24 36M
xenoRefSeqAli.sql 09-Jul-2017 08:24 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 08:24 34M