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 -
xenoRefSeqAli.txt.gz 2020-08-21 05:07 1.7M
xenoRefSeqAli.sql 2020-08-21 05:07 2.1K
xenoRefGene.txt.gz 2020-08-21 05:05 1.7M
xenoRefGene.sql 2020-08-21 05:05 2.0K
xenoRefFlat.txt.gz 2020-08-21 05:07 1.5M
xenoRefFlat.sql 2020-08-21 05:07 1.7K
xenoMrna.txt.gz 2020-08-21 04:40 37M
xenoMrna.sql 2020-08-21 04:40 2.1K
trackDb_pushedout.txt.gz 2022-11-29 11:10 36K
trackDb_pushedout.sql 2022-11-29 11:10 2.1K
trackDb.txt.gz 2023-03-28 13:47 36K
trackDb.sql 2023-03-28 13:47 2.1K
tableList.txt.gz 2024-04-21 03:35 4.3K
tableList.sql 2024-04-21 03:35 1.6K
tableDescriptions.txt.gz 2024-04-20 02:03 6.2K
tableDescriptions.sql 2024-04-20 02:03 1.5K
simpleRepeat.txt.gz 2012-01-05 11:46 1.2M
simpleRepeat.sql 2012-01-05 11:46 1.9K
rmsk.txt.gz 2012-01-05 11:45 2.3M
rmsk.sql 2012-01-05 11:45 1.8K
refSeqAli.txt.gz 2020-08-21 05:07 2.6M
refSeqAli.sql 2020-08-21 05:07 2.1K
refGene.txt.gz 2020-08-21 04:52 2.3M
refGene.sql 2020-08-21 04:52 1.9K
refFlat.txt.gz 2020-08-21 05:05 2.1M
refFlat.sql 2020-08-21 05:05 1.7K
pubsBingBlatPsl.txt.gz 2014-01-26 09:30 603K
pubsBingBlatPsl.sql 2014-01-26 09:30 2.2K
pubsBingBlat.txt.gz 2014-01-26 09:30 762K
pubsBingBlat.sql 2014-01-26 09:30 2.4K
phyloP7way.txt.gz 2012-01-05 11:46 2.3M
phyloP7way.sql 2012-01-05 11:46 1.7K
phastConsElements7way.txt.gz 2012-01-05 11:44 3.7M
phastConsElements7way.sql 2012-01-05 11:44 1.5K
phastCons7way.txt.gz 2012-01-05 11:48 2.3M
phastCons7way.sql 2012-01-05 11:48 1.7K
nestedRepeats.txt.gz 2012-01-05 11:46 93K
nestedRepeats.sql 2012-01-05 11:46 1.9K
multiz7waySummary.txt.gz 2012-01-05 11:43 1.1M
multiz7waySummary.sql 2012-01-05 11:43 1.5K
multiz7wayFrames.txt.gz 2012-01-05 11:45 3.7M
multiz7wayFrames.sql 2012-01-05 11:45 1.7K
multiz7way.txt.gz 2012-01-05 11:44 5.5M
multiz7way.sql 2012-01-05 11:44 1.5K
mrnaOrientInfo.txt.gz 2020-08-21 05:07 845K
mrnaOrientInfo.sql 2020-08-21 05:07 1.8K
microsat.txt.gz 2015-08-23 12:08 3.0K
microsat.sql 2015-08-23 12:08 1.5K
locusName.txt.gz 2016-11-06 06:22 2.4M
locusName.sql 2016-11-06 06:22 1.5K
history.txt.gz 2012-01-05 11:44 1.5K
history.sql 2012-01-05 11:44 1.5K
hgFindSpec_pushedout.txt.gz 2022-11-29 11:10 865
hgFindSpec_pushedout.sql 2022-11-29 11:10 1.8K
hgFindSpec.txt.gz 2023-03-28 13:47 867
hgFindSpec.sql 2023-03-28 13:47 1.8K
grp.txt.gz 2014-03-02 03:40 209
grp.sql 2014-03-02 03:40 1.3K
gold.txt.gz 2012-01-05 11:46 56K
gold.sql 2012-01-05 11:46 1.6K
gc5BaseBw.txt.gz 2012-01-05 11:43 60
gc5BaseBw.sql 2012-01-05 11:43 1.2K
gbLoaded.txt.gz 2020-08-21 05:07 95K
gbLoaded.sql 2020-08-21 05:07 1.6K
gap.txt.gz 2012-01-05 11:48 28
gap.sql 2012-01-05 11:48 1.5K
extFile.txt.gz 2012-01-05 11:46 246
extFile.sql 2012-01-05 11:46 1.3K
estOrientInfo.txt.gz 2016-06-05 09:17 4.1M
estOrientInfo.sql 2016-06-05 09:17 1.8K
ensemblToGeneName.txt.gz 2012-01-05 11:45 257K
ensemblToGeneName.sql 2012-01-05 11:45 1.3K
ensemblSource.txt.gz 2012-01-05 11:46 176K
ensemblSource.sql 2012-01-05 11:46 1.3K
ensPep.txt.gz 2012-01-05 11:44 5.0M
ensPep.sql 2012-01-05 11:44 1.3K
ensGtp.txt.gz 2012-01-05 11:43 252K
ensGtp.sql 2012-01-05 11:43 1.4K
ensGene.txt.gz 2012-01-05 11:43 2.1M
ensGene.sql 2012-01-05 11:43 1.8K
crisprTargets.txt.gz 2016-11-06 06:22 60
crisprTargets.sql 2016-11-06 06:22 1.3K
crisprRanges.txt.gz 2016-11-06 06:22 322K
crisprRanges.sql 2016-11-06 06:22 1.4K
chromInfo.txt.gz 2012-01-05 11:46 127
chromInfo.sql 2012-01-05 11:46 1.3K
chrX_mrna.txt.gz 2020-08-21 04:40 47K
chrX_mrna.sql 2020-08-21 04:40 2.1K
chrX_intronEst.txt.gz 2016-06-05 09:17 1.5M
chrX_intronEst.sql 2016-06-05 09:17 2.1K
chrX_est.txt.gz 2016-06-05 09:17 1.8M
chrX_est.sql 2016-06-05 09:17 2.1K
chrV_mrna.txt.gz 2018-01-07 06:38 41K
chrV_mrna.sql 2018-01-07 06:38 2.1K
chrV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrV_intronEst.sql 2016-06-05 09:17 2.1K
chrV_est.txt.gz 2016-06-05 09:17 2.3M
chrV_est.sql 2016-06-05 09:17 2.1K
chrM_mrna.txt.gz 2012-01-05 11:43 34
chrM_mrna.sql 2012-01-05 11:43 2.0K
chrM_intronEst.txt.gz 2012-01-05 11:43 39
chrM_intronEst.sql 2012-01-05 11:43 2.0K
chrM_est.txt.gz 2016-06-05 09:17 52K
chrM_est.sql 2016-06-05 09:17 2.1K
chrI_mrna.txt.gz 2020-05-07 16:26 41K
chrI_mrna.sql 2020-05-07 16:26 2.1K
chrI_intronEst.txt.gz 2016-06-05 09:17 2.2M
chrI_intronEst.sql 2016-06-05 09:17 2.1K
chrI_est.txt.gz 2016-06-05 09:17 3.0M
chrI_est.sql 2016-06-05 09:17 2.1K
chrIV_mrna.txt.gz 2020-08-21 04:40 119K
chrIV_mrna.sql 2020-08-21 04:40 2.1K
chrIV_intronEst.txt.gz 2016-06-05 09:17 1.8M
chrIV_intronEst.sql 2016-06-05 09:17 2.1K
chrIV_est.txt.gz 2016-06-05 09:17 2.3M
chrIV_est.sql 2016-06-05 09:17 2.1K
chrII_mrna.txt.gz 2020-08-21 04:40 30K
chrII_mrna.sql 2020-08-21 04:40 2.1K
chrII_intronEst.txt.gz 2016-06-05 09:17 2.1M
chrII_intronEst.sql 2016-06-05 09:17 2.1K
chrII_est.txt.gz 2016-06-05 09:17 2.6M
chrII_est.sql 2016-06-05 09:17 2.1K
chrIII_mrna.txt.gz 2020-08-21 04:40 40K
chrIII_mrna.sql 2020-08-21 04:40 2.1K
chrIII_intronEst.txt.gz 2016-06-05 09:17 1.9M
chrIII_intronEst.sql 2016-06-05 09:17 2.1K
chrIII_est.txt.gz 2016-06-05 09:17 2.4M
chrIII_est.sql 2016-06-05 09:17 2.1K
blastHg18KG.txt.gz 2012-07-15 08:13 906K
blastHg18KG.sql 2012-07-15 08:13 2.1K
bigFiles.txt.gz 2024-04-21 03:35 87
bigFiles.sql 2024-04-21 03:35 1.4K
augustusGene.txt.gz 2015-07-26 11:22 1.3M
augustusGene.sql 2015-07-26 11:22 1.9K
all_mrna.txt.gz 2020-08-21 04:40 318K
all_mrna.sql 2020-08-21 04:40 2.1K
all_est.txt.gz 2016-06-05 09:16 14M
all_est.sql 2016-06-05 09:16 2.1K