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 -
gbWarn.txt.gz 2017-07-21 10:14 31
imageClone.txt.gz 2017-07-21 10:14 35
sex.txt.gz 2017-07-21 10:14 39
cell.txt.gz 2017-07-21 10:13 40
gc5BaseBw.txt.gz 2017-07-21 10:14 62
bigFiles.txt.gz 2024-11-17 03:15 65
grp.txt.gz 2017-07-21 10:14 213
development.txt.gz 2017-07-21 10:13 442
tissue.txt.gz 2017-07-21 10:14 617
history.txt.gz 2017-07-21 10:14 785
hgFindSpec.txt.gz 2024-07-25 09:34 885
library.txt.gz 2017-07-21 10:14 914
gc5BaseBw.sql 2017-07-21 10:14 1.3K
gbWarn.sql 2017-07-21 10:14 1.3K
ensPep.sql 2021-05-25 14:25 1.3K
grp.sql 2017-07-21 10:14 1.3K
ensemblSource.sql 2021-05-25 14:25 1.4K
bigFiles.sql 2024-11-17 03:15 1.4K
chromInfo.sql 2017-07-21 10:13 1.4K
cds.sql 2017-07-21 10:13 1.4K
sex.sql 2017-07-21 10:14 1.4K
cell.sql 2017-07-21 10:13 1.4K
author.sql 2017-07-21 10:13 1.4K
source.sql 2017-07-21 10:14 1.4K
tissue.sql 2017-07-21 10:14 1.4K
gbExtFile.sql 2017-07-21 10:13 1.4K
keyword.sql 2017-07-21 10:14 1.4K
library.sql 2017-07-21 10:14 1.4K
geneName.sql 2017-07-21 10:14 1.4K
organism.sql 2017-07-21 10:14 1.4K
ensemblToGeneName.sql 2021-05-25 14:25 1.4K
mrnaClone.sql 2017-07-21 10:14 1.4K
description.sql 2017-07-21 10:13 1.4K
development.sql 2017-07-21 10:13 1.4K
productName.sql 2017-07-21 10:14 1.4K
chromAlias.sql 2017-07-21 10:13 1.4K
ucscToINSDC.sql 2017-07-21 10:14 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToRefSeq.sql 2017-07-21 10:14 1.4K
ensGtp.sql 2021-05-25 14:25 1.4K
gbMiscDiff.sql 2017-07-21 10:13 1.5K
gbMiscDiff.txt.gz 2017-07-21 10:13 1.5K
microsat.sql 2017-07-21 10:14 1.5K
refSeqSummary.sql 2017-07-21 10:14 1.5K
imageClone.sql 2017-07-21 10:14 1.5K
windowmaskerSdust.sql 2017-07-21 10:14 1.5K
cytoBandIdeo.sql 2017-07-21 10:13 1.5K
chainCe11Link.sql 2017-07-21 10:13 1.5K
chainStrPur2Link.sql 2017-07-21 10:13 1.5K
tableList.sql 2024-11-17 03:15 1.6K
history.sql 2017-07-21 10:14 1.6K
gbLoaded.sql 2017-07-21 10:13 1.6K
gap.sql 2017-07-21 10:13 1.6K
refSeqStatus.sql 2017-07-21 10:14 1.6K
gold.sql 2017-07-21 10:14 1.7K
genscan.sql 2017-07-21 10:14 1.7K
cpgIslandExt.sql 2017-07-21 10:13 1.7K
chainCe11.sql 2017-07-21 10:13 1.7K
gbSeq.sql 2017-07-21 10:13 1.7K
refFlat.sql 2017-07-21 10:14 1.7K
chainStrPur2.sql 2017-07-21 10:13 1.7K
cpgIslandExtUnmasked.sql 2017-07-21 10:13 1.7K
xenoRefFlat.sql 2017-07-21 10:14 1.7K
refLink.sql 2017-07-21 10:14 1.7K
hgFindSpec.sql 2024-07-25 09:34 1.8K
microsat.txt.gz 2017-07-21 10:14 1.8K
estOrientInfo.sql 2017-07-21 10:13 1.8K
mrnaOrientInfo.sql 2017-07-21 10:14 1.8K
rmsk.sql 2017-07-21 10:14 1.9K
gbStatus.sql 2017-07-21 10:13 1.9K
refGene.sql 2017-07-21 10:14 1.9K
simpleRepeat.sql 2017-07-21 10:14 1.9K
nestedRepeats.sql 2017-07-21 10:14 1.9K
xenoRefGene.sql 2017-07-21 10:14 1.9K
ensGene.sql 2021-05-25 14:25 1.9K
trackDb.sql 2024-07-25 09:34 2.1K
netCe11.sql 2017-07-21 10:14 2.1K
netStrPur2.sql 2017-07-21 10:14 2.1K
all_est.sql 2017-07-21 10:13 2.1K
all_mrna.sql 2017-07-21 10:13 2.1K
intronEst.sql 2017-07-21 10:14 2.1K
refSeqAli.sql 2017-07-21 10:14 2.1K
xenoRefSeqAli.sql 2017-07-21 10:14 2.1K
gbCdnaInfo.sql 2017-07-21 10:13 2.6K
tableList.txt.gz 2024-11-17 03:15 3.6K
keyword.txt.gz 2017-07-21 10:14 3.6K
ensemblToGeneName.txt.gz 2021-05-25 14:25 5.8K
tableDescriptions.txt.gz 2024-11-16 02:03 7.3K
cytoBandIdeo.txt.gz 2017-07-21 10:13 7.6K
chromInfo.txt.gz 2017-07-21 10:13 7.8K
gbExtFile.txt.gz 2017-07-21 10:13 10K
ucscToRefSeq.txt.gz 2017-07-21 10:14 11K
ucscToINSDC.txt.gz 2017-07-21 10:14 11K
chromAlias.txt.gz 2017-07-21 10:13 13K
gbLoaded.txt.gz 2017-07-21 10:13 15K
cpgIslandExt.txt.gz 2017-07-21 10:13 28K
cpgIslandExtUnmasked.txt.gz 2017-07-21 10:13 36K
trackDb.txt.gz 2024-07-25 09:34 45K
ensemblSource.txt.gz 2021-05-25 14:25 51K
gap.txt.gz 2017-07-21 10:13 59K
refFlat.txt.gz 2017-07-21 10:14 87K
refGene.txt.gz 2017-07-21 10:14 96K
gold.txt.gz 2017-07-21 10:14 100K
refSeqAli.txt.gz 2017-07-21 10:14 102K
mrnaOrientInfo.txt.gz 2017-07-21 10:14 149K
ensGtp.txt.gz 2021-05-25 14:25 184K
nestedRepeats.txt.gz 2017-07-21 10:14 205K
netCe11.txt.gz 2017-07-21 10:14 304K
organism.txt.gz 2017-07-21 10:14 306K
source.txt.gz 2017-07-21 10:14 313K
chainCe11.txt.gz 2017-07-21 10:13 315K
genscan.txt.gz 2017-07-21 10:14 415K
all_mrna.txt.gz 2017-07-21 10:13 676K
chainCe11Link.txt.gz 2017-07-21 10:13 706K
netStrPur2.txt.gz 2017-07-21 10:14 791K
simpleRepeat.txt.gz 2017-07-21 10:14 1.1M
ensGene.txt.gz 2021-05-25 14:25 1.2M
refSeqStatus.txt.gz 2017-07-21 10:14 1.5M
chainStrPur2.txt.gz 2017-07-21 10:13 1.5M
cds.txt.gz 2017-07-21 10:13 2.1M
rmsk.txt.gz 2017-07-21 10:14 3.2M
ensPep.txt.gz 2021-05-25 14:25 3.3M
chainStrPur2Link.txt.gz 2017-07-21 10:13 3.5M
productName.txt.gz 2017-07-21 10:14 3.6M
xenoRefSeqAli.txt.gz 2017-07-21 10:14 3.9M
author.txt.gz 2017-07-21 10:13 4.1M
geneName.txt.gz 2017-07-21 10:14 4.2M
xenoRefFlat.txt.gz 2017-07-21 10:14 4.2M
xenoRefGene.txt.gz 2017-07-21 10:14 4.7M
refSeqSummary.txt.gz 2017-07-21 10:14 5.2M
mrnaClone.txt.gz 2017-07-21 10:14 5.7M
windowmaskerSdust.txt.gz 2017-07-21 10:14 7.5M
refLink.txt.gz 2017-07-21 10:14 11M
estOrientInfo.txt.gz 2017-07-21 10:13 11M
gbStatus.txt.gz 2017-07-21 10:13 11M
description.txt.gz 2017-07-21 10:13 13M
gbCdnaInfo.txt.gz 2017-07-21 10:13 22M
intronEst.txt.gz 2017-07-21 10:14 26M
gbSeq.txt.gz 2017-07-21 10:13 29M
all_est.txt.gz 2017-07-21 10:13 39M