This directory contains a dump of the UCSC genome annotation database for the
Apr. 2011 (Kyoto KH/ci3) assembly of the C. intestinalis genome
(ci3, Kyoto KH) .
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/49
http://www.ncbi.nlm.nih.gov/genome/assembly/527578
http://www.ncbi.nlm.nih.gov/bioproject/187185
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=ci3
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/ci3/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/ci3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ci3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ci3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ci3/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 ci3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ci3 --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 2017-07-21 10:14 3.9M
xenoRefSeqAli.sql 2017-07-21 10:14 2.1K
xenoRefGene.txt.gz 2017-07-21 10:14 4.7M
xenoRefGene.sql 2017-07-21 10:14 1.9K
xenoRefFlat.txt.gz 2017-07-21 10:14 4.2M
xenoRefFlat.sql 2017-07-21 10:14 1.7K
windowmaskerSdust.txt.gz 2017-07-21 10:14 7.5M
windowmaskerSdust.sql 2017-07-21 10:14 1.5K
ucscToRefSeq.txt.gz 2017-07-21 10:14 11K
ucscToRefSeq.sql 2017-07-21 10:14 1.4K
ucscToINSDC.txt.gz 2017-07-21 10:14 11K
ucscToINSDC.sql 2017-07-21 10:14 1.4K
trackDb.txt.gz 2024-07-25 09:34 45K
trackDb.sql 2024-07-25 09:34 2.1K
tissue.txt.gz 2017-07-21 10:14 617
tissue.sql 2017-07-21 10:14 1.4K
tableList.txt.gz 2024-11-17 03:15 3.6K
tableList.sql 2024-11-17 03:15 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 7.3K
tableDescriptions.sql 2024-11-16 02:03 1.4K
source.txt.gz 2017-07-21 10:14 313K
source.sql 2017-07-21 10:14 1.4K
simpleRepeat.txt.gz 2017-07-21 10:14 1.1M
simpleRepeat.sql 2017-07-21 10:14 1.9K
sex.txt.gz 2017-07-21 10:14 39
sex.sql 2017-07-21 10:14 1.4K
rmsk.txt.gz 2017-07-21 10:14 3.2M
rmsk.sql 2017-07-21 10:14 1.9K
refSeqSummary.txt.gz 2017-07-21 10:14 5.2M
refSeqSummary.sql 2017-07-21 10:14 1.5K
refSeqStatus.txt.gz 2017-07-21 10:14 1.5M
refSeqStatus.sql 2017-07-21 10:14 1.6K
refSeqAli.txt.gz 2017-07-21 10:14 102K
refSeqAli.sql 2017-07-21 10:14 2.1K
refLink.txt.gz 2017-07-21 10:14 11M
refLink.sql 2017-07-21 10:14 1.7K
refGene.txt.gz 2017-07-21 10:14 96K
refGene.sql 2017-07-21 10:14 1.9K
refFlat.txt.gz 2017-07-21 10:14 87K
refFlat.sql 2017-07-21 10:14 1.7K
productName.txt.gz 2017-07-21 10:14 3.6M
productName.sql 2017-07-21 10:14 1.4K
organism.txt.gz 2017-07-21 10:14 306K
organism.sql 2017-07-21 10:14 1.4K
netStrPur2.txt.gz 2017-07-21 10:14 791K
netStrPur2.sql 2017-07-21 10:14 2.1K
netCe11.txt.gz 2017-07-21 10:14 304K
netCe11.sql 2017-07-21 10:14 2.1K
nestedRepeats.txt.gz 2017-07-21 10:14 205K
nestedRepeats.sql 2017-07-21 10:14 1.9K
mrnaOrientInfo.txt.gz 2017-07-21 10:14 149K
mrnaOrientInfo.sql 2017-07-21 10:14 1.8K
mrnaClone.txt.gz 2017-07-21 10:14 5.7M
mrnaClone.sql 2017-07-21 10:14 1.4K
microsat.txt.gz 2017-07-21 10:14 1.8K
microsat.sql 2017-07-21 10:14 1.5K
library.txt.gz 2017-07-21 10:14 914
library.sql 2017-07-21 10:14 1.4K
keyword.txt.gz 2017-07-21 10:14 3.6K
keyword.sql 2017-07-21 10:14 1.4K
intronEst.txt.gz 2017-07-21 10:14 26M
intronEst.sql 2017-07-21 10:14 2.1K
imageClone.txt.gz 2017-07-21 10:14 35
imageClone.sql 2017-07-21 10:14 1.5K
history.txt.gz 2017-07-21 10:14 785
history.sql 2017-07-21 10:14 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 885
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2017-07-21 10:14 213
grp.sql 2017-07-21 10:14 1.3K
gold.txt.gz 2017-07-21 10:14 100K
gold.sql 2017-07-21 10:14 1.7K
genscan.txt.gz 2017-07-21 10:14 415K
genscan.sql 2017-07-21 10:14 1.7K
geneName.txt.gz 2017-07-21 10:14 4.2M
geneName.sql 2017-07-21 10:14 1.4K
gc5BaseBw.txt.gz 2017-07-21 10:14 62
gc5BaseBw.sql 2017-07-21 10:14 1.3K
gbWarn.txt.gz 2017-07-21 10:14 31
gbWarn.sql 2017-07-21 10:14 1.3K
gbStatus.txt.gz 2017-07-21 10:13 11M
gbStatus.sql 2017-07-21 10:13 1.9K
gbSeq.txt.gz 2017-07-21 10:13 29M
gbSeq.sql 2017-07-21 10:13 1.7K
gbMiscDiff.txt.gz 2017-07-21 10:13 1.5K
gbMiscDiff.sql 2017-07-21 10:13 1.5K
gbLoaded.txt.gz 2017-07-21 10:13 15K
gbLoaded.sql 2017-07-21 10:13 1.6K
gbExtFile.txt.gz 2017-07-21 10:13 10K
gbExtFile.sql 2017-07-21 10:13 1.4K
gbCdnaInfo.txt.gz 2017-07-21 10:13 22M
gbCdnaInfo.sql 2017-07-21 10:13 2.6K
gap.txt.gz 2017-07-21 10:13 59K
gap.sql 2017-07-21 10:13 1.6K
estOrientInfo.txt.gz 2017-07-21 10:13 11M
estOrientInfo.sql 2017-07-21 10:13 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:25 5.8K
ensemblToGeneName.sql 2021-05-25 14:25 1.4K
ensemblSource.txt.gz 2021-05-25 14:25 51K
ensemblSource.sql 2021-05-25 14:25 1.4K
ensPep.txt.gz 2021-05-25 14:25 3.3M
ensPep.sql 2021-05-25 14:25 1.3K
ensGtp.txt.gz 2021-05-25 14:25 184K
ensGtp.sql 2021-05-25 14:25 1.4K
ensGene.txt.gz 2021-05-25 14:25 1.2M
ensGene.sql 2021-05-25 14:25 1.9K
development.txt.gz 2017-07-21 10:13 442
development.sql 2017-07-21 10:13 1.4K
description.txt.gz 2017-07-21 10:13 13M
description.sql 2017-07-21 10:13 1.4K
cytoBandIdeo.txt.gz 2017-07-21 10:13 7.6K
cytoBandIdeo.sql 2017-07-21 10:13 1.5K
cpgIslandExtUnmasked.txt.gz 2017-07-21 10:13 36K
cpgIslandExtUnmasked.sql 2017-07-21 10:13 1.7K
cpgIslandExt.txt.gz 2017-07-21 10:13 28K
cpgIslandExt.sql 2017-07-21 10:13 1.7K
chromInfo.txt.gz 2017-07-21 10:13 7.8K
chromInfo.sql 2017-07-21 10:13 1.4K
chromAlias.txt.gz 2017-07-21 10:13 13K
chromAlias.sql 2017-07-21 10:13 1.4K
chainStrPur2Link.txt.gz 2017-07-21 10:13 3.5M
chainStrPur2Link.sql 2017-07-21 10:13 1.5K
chainStrPur2.txt.gz 2017-07-21 10:13 1.5M
chainStrPur2.sql 2017-07-21 10:13 1.7K
chainCe11Link.txt.gz 2017-07-21 10:13 706K
chainCe11Link.sql 2017-07-21 10:13 1.5K
chainCe11.txt.gz 2017-07-21 10:13 315K
chainCe11.sql 2017-07-21 10:13 1.7K
cell.txt.gz 2017-07-21 10:13 40
cell.sql 2017-07-21 10:13 1.4K
cds.txt.gz 2017-07-21 10:13 2.1M
cds.sql 2017-07-21 10:13 1.4K
bigFiles.txt.gz 2024-11-17 03:15 65
bigFiles.sql 2024-11-17 03:15 1.4K
author.txt.gz 2017-07-21 10:13 4.1M
author.sql 2017-07-21 10:13 1.4K
all_mrna.txt.gz 2017-07-21 10:13 676K
all_mrna.sql 2017-07-21 10:13 2.1K
all_est.txt.gz 2017-07-21 10:13 39M
all_est.sql 2017-07-21 10:13 2.1K