This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (WS220/ce10) assembly of the C. elegans genome
(ce10, Washington University School of Medicine GSC and Sanger Institute WS220).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Genome Sequencing Center at the
Washington University in St. Louis (WUSTL) School of Medicine and
the Sanger Institute. For more information on the
C. elegans genome, see the WUSTL project website at
http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+elegans.
and WormBase information:
http://wiki.wormbase.org/index.php/Caenorhabditis_elegans
This UCSC sequence data was downloaded from:
ftp://ftp.sanger.ac.uk/pub/wormbase/WS220/genomes/c_elegans/
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=ce10
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
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/ce10/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/ce10/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ce10/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce10/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 ce10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ce10 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
------------------------------------------------------------------------
The C. elegans sequence is made freely available to the community by the
Genome Sequencing Center at the WUSTL School of Medicine. Please see the
WUSTL data use policy at http://genome.wustl.edu/data.cgi for data use
restrictions and citation information.
------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
gap.txt.gz 2012-01-05 11:48 28
chrM_mrna.txt.gz 2012-01-05 11:43 34
chrM_intronEst.txt.gz 2012-01-05 11:43 39
crisprTargets.txt.gz 2016-11-06 06:22 60
gc5BaseBw.txt.gz 2012-01-05 11:43 60
bigFiles.txt.gz 2024-04-21 03:35 87
chromInfo.txt.gz 2012-01-05 11:46 127
grp.txt.gz 2014-03-02 03:40 209
extFile.txt.gz 2012-01-05 11:46 246
hgFindSpec_pushedout.txt.gz 2022-11-29 11:10 865
hgFindSpec.txt.gz 2023-03-28 13:47 867
gc5BaseBw.sql 2012-01-05 11:43 1.2K
ensPep.sql 2012-01-05 11:44 1.3K
ensemblSource.sql 2012-01-05 11:46 1.3K
crisprTargets.sql 2016-11-06 06:22 1.3K
chromInfo.sql 2012-01-05 11:46 1.3K
ensemblToGeneName.sql 2012-01-05 11:45 1.3K
grp.sql 2014-03-02 03:40 1.3K
extFile.sql 2012-01-05 11:46 1.3K
ensGtp.sql 2012-01-05 11:43 1.4K
bigFiles.sql 2024-04-21 03:35 1.4K
crisprRanges.sql 2016-11-06 06:22 1.4K
tableDescriptions.sql 2024-04-20 02:03 1.5K
multiz7way.sql 2012-01-05 11:44 1.5K
microsat.sql 2015-08-23 12:08 1.5K
locusName.sql 2016-11-06 06:22 1.5K
phastConsElements7way.sql 2012-01-05 11:44 1.5K
history.sql 2012-01-05 11:44 1.5K
multiz7waySummary.sql 2012-01-05 11:43 1.5K
gap.sql 2012-01-05 11:48 1.5K
history.txt.gz 2012-01-05 11:44 1.5K
tableList.sql 2024-04-21 03:35 1.6K
gold.sql 2012-01-05 11:46 1.6K
gbLoaded.sql 2020-08-21 05:07 1.6K
multiz7wayFrames.sql 2012-01-05 11:45 1.7K
phyloP7way.sql 2012-01-05 11:46 1.7K
phastCons7way.sql 2012-01-05 11:48 1.7K
refFlat.sql 2020-08-21 05:05 1.7K
xenoRefFlat.sql 2020-08-21 05:07 1.7K
hgFindSpec.sql 2023-03-28 13:47 1.8K
estOrientInfo.sql 2016-06-05 09:17 1.8K
hgFindSpec_pushedout.sql 2022-11-29 11:10 1.8K
rmsk.sql 2012-01-05 11:45 1.8K
mrnaOrientInfo.sql 2020-08-21 05:07 1.8K
ensGene.sql 2012-01-05 11:43 1.8K
simpleRepeat.sql 2012-01-05 11:46 1.9K
nestedRepeats.sql 2012-01-05 11:46 1.9K
augustusGene.sql 2015-07-26 11:22 1.9K
refGene.sql 2020-08-21 04:52 1.9K
xenoRefGene.sql 2020-08-21 05:05 2.0K
chrM_mrna.sql 2012-01-05 11:43 2.0K
chrM_intronEst.sql 2012-01-05 11:43 2.0K
trackDb.sql 2023-03-28 13:47 2.1K
trackDb_pushedout.sql 2022-11-29 11:10 2.1K
chrI_est.sql 2016-06-05 09:17 2.1K
chrM_est.sql 2016-06-05 09:17 2.1K
chrV_est.sql 2016-06-05 09:17 2.1K
chrX_est.sql 2016-06-05 09:17 2.1K
chrII_est.sql 2016-06-05 09:17 2.1K
chrIV_est.sql 2016-06-05 09:17 2.1K
chrV_mrna.sql 2018-01-07 06:38 2.1K
chrIII_est.sql 2016-06-05 09:17 2.1K
all_est.sql 2016-06-05 09:16 2.1K
chrI_intronEst.sql 2016-06-05 09:17 2.1K
chrV_intronEst.sql 2016-06-05 09:17 2.1K
chrX_intronEst.sql 2016-06-05 09:17 2.1K
chrII_intronEst.sql 2016-06-05 09:17 2.1K
chrIV_intronEst.sql 2016-06-05 09:17 2.1K
blastHg18KG.sql 2012-07-15 08:13 2.1K
chrIII_intronEst.sql 2016-06-05 09:17 2.1K
chrI_mrna.sql 2020-05-07 16:26 2.1K
chrX_mrna.sql 2020-08-21 04:40 2.1K
chrII_mrna.sql 2020-08-21 04:40 2.1K
chrIV_mrna.sql 2020-08-21 04:40 2.1K
chrIII_mrna.sql 2020-08-21 04:40 2.1K
all_mrna.sql 2020-08-21 04:40 2.1K
xenoMrna.sql 2020-08-21 04:40 2.1K
refSeqAli.sql 2020-08-21 05:07 2.1K
xenoRefSeqAli.sql 2020-08-21 05:07 2.1K
pubsBingBlatPsl.sql 2014-01-26 09:30 2.2K
pubsBingBlat.sql 2014-01-26 09:30 2.4K
microsat.txt.gz 2015-08-23 12:08 3.0K
tableList.txt.gz 2024-04-21 03:35 4.3K
tableDescriptions.txt.gz 2024-04-20 02:03 6.2K
chrII_mrna.txt.gz 2020-08-21 04:40 30K
trackDb_pushedout.txt.gz 2022-11-29 11:10 36K
trackDb.txt.gz 2023-03-28 13:47 36K
chrIII_mrna.txt.gz 2020-08-21 04:40 40K
chrI_mrna.txt.gz 2020-05-07 16:26 41K
chrV_mrna.txt.gz 2018-01-07 06:38 41K
chrX_mrna.txt.gz 2020-08-21 04:40 47K
chrM_est.txt.gz 2016-06-05 09:17 52K
gold.txt.gz 2012-01-05 11:46 56K
nestedRepeats.txt.gz 2012-01-05 11:46 93K
gbLoaded.txt.gz 2020-08-21 05:07 95K
chrIV_mrna.txt.gz 2020-08-21 04:40 119K
ensemblSource.txt.gz 2012-01-05 11:46 176K
ensGtp.txt.gz 2012-01-05 11:43 252K
ensemblToGeneName.txt.gz 2012-01-05 11:45 257K
all_mrna.txt.gz 2020-08-21 04:40 318K
crisprRanges.txt.gz 2016-11-06 06:22 322K
pubsBingBlatPsl.txt.gz 2014-01-26 09:30 603K
pubsBingBlat.txt.gz 2014-01-26 09:30 762K
mrnaOrientInfo.txt.gz 2020-08-21 05:07 845K
blastHg18KG.txt.gz 2012-07-15 08:13 906K
multiz7waySummary.txt.gz 2012-01-05 11:43 1.1M
simpleRepeat.txt.gz 2012-01-05 11:46 1.2M
augustusGene.txt.gz 2015-07-26 11:22 1.3M
chrX_intronEst.txt.gz 2016-06-05 09:17 1.5M
xenoRefFlat.txt.gz 2020-08-21 05:07 1.5M
xenoRefGene.txt.gz 2020-08-21 05:05 1.7M
xenoRefSeqAli.txt.gz 2020-08-21 05:07 1.7M
chrIV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrX_est.txt.gz 2016-06-05 09:17 1.8M
chrIII_intronEst.txt.gz 2016-06-05 09:17 1.9M
ensGene.txt.gz 2012-01-05 11:43 2.1M
refFlat.txt.gz 2020-08-21 05:05 2.1M
chrII_intronEst.txt.gz 2016-06-05 09:17 2.1M
chrI_intronEst.txt.gz 2016-06-05 09:17 2.2M
chrIV_est.txt.gz 2016-06-05 09:17 2.3M
phastCons7way.txt.gz 2012-01-05 11:48 2.3M
rmsk.txt.gz 2012-01-05 11:45 2.3M
chrV_est.txt.gz 2016-06-05 09:17 2.3M
refGene.txt.gz 2020-08-21 04:52 2.3M
phyloP7way.txt.gz 2012-01-05 11:46 2.3M
chrIII_est.txt.gz 2016-06-05 09:17 2.4M
locusName.txt.gz 2016-11-06 06:22 2.4M
chrII_est.txt.gz 2016-06-05 09:17 2.6M
refSeqAli.txt.gz 2020-08-21 05:07 2.6M
chrI_est.txt.gz 2016-06-05 09:17 3.0M
multiz7wayFrames.txt.gz 2012-01-05 11:45 3.7M
phastConsElements7way.txt.gz 2012-01-05 11:44 3.7M
estOrientInfo.txt.gz 2016-06-05 09:17 4.1M
ensPep.txt.gz 2012-01-05 11:44 5.0M
multiz7way.txt.gz 2012-01-05 11:44 5.5M
all_est.txt.gz 2016-06-05 09:16 14M
xenoMrna.txt.gz 2020-08-21 04:40 37M