This directory contains a dump of the UCSC genome annotation database for
the Apr. 2011 (SacCer_Apr2011/sacCer3) assembly of the S. cerevisiae genome
(sacCer3, Saccharomyces cerevisiae S288c assembly from
Saccharomyces Genome Database (GCA_000146055.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly is based on sequence dated April 2011 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/fungi/Saccharomyces_cerevisiae/SacCer_Apr2011/
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=sacCer3
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/sacCer3/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/sacCer3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/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 sacCer3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sacCer3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 -
choExpDistance.txt.gz 2011-10-06 16:16 34M
pslChainAWRI1631.txt.gz 2011-10-06 16:15 3.3M
sgdPep.txt.gz 2011-10-06 16:15 1.7M
ensPep.txt.gz 2021-05-25 14:46 1.7M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:08 1.6M
transRegCode.txt.gz 2011-10-06 16:15 1.4M
xenoRefSeqAli.txt.gz 2020-08-20 09:46 1.2M
xenoRefGene.txt.gz 2020-08-20 09:46 1.1M
xenoRefFlat.txt.gz 2020-08-20 09:46 1.0M
all_est.txt.gz 2012-05-28 14:19 962K
sgdBlastTab.txt.gz 2011-10-06 16:15 943K
multiz7way.txt.gz 2011-10-06 16:15 669K
ncbiRefSeqLink.txt.gz 2021-02-10 15:45 661K
phastConsElements7way.txt.gz 2011-10-06 16:15 503K
blastHg18KG.txt.gz 2011-10-06 16:15 350K
sgdDescription.txt.gz 2011-10-06 16:17 337K
estOrientInfo.txt.gz 2012-05-28 14:19 306K
phastCons7way.txt.gz 2011-10-06 16:15 305K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:45 158K
ensGene.txt.gz 2021-05-25 14:46 150K
chrIV_est.txt.gz 2012-05-28 14:19 150K
transRegCodeProbe.txt.gz 2011-10-06 16:15 143K
locusName.txt.gz 2016-11-06 09:28 141K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:45 140K
ncbiRefSeq.txt.gz 2021-02-10 15:45 140K
sgdGene.txt.gz 2011-10-06 16:18 131K
oregannoAttr.txt.gz 2016-05-15 11:29 118K
augustusGene.txt.gz 2015-07-26 17:28 109K
sgdCanonical.txt.gz 2011-10-06 16:18 102K
chrXV_est.txt.gz 2012-05-28 14:19 100K
gbLoaded.txt.gz 2020-08-20 09:58 90K
seqNcbiRefSeq.txt.gz 2021-02-10 16:08 88K
ceBlastTab.txt.gz 2011-10-06 16:15 87K
chrXVI_est.txt.gz 2012-05-28 14:19 85K
oreganno.txt.gz 2016-05-15 11:29 85K
dmBlastTab.txt.gz 2011-10-06 16:17 85K
chrVII_est.txt.gz 2012-05-28 14:19 84K
multiz7wayFrames.txt.gz 2011-10-06 16:18 83K
oregannoLink.txt.gz 2016-05-15 11:29 83K
chrXII_est.txt.gz 2012-05-28 14:19 81K
chrII_est.txt.gz 2012-05-28 14:19 71K
chrXIII_est.txt.gz 2012-05-28 14:19 70K
drBlastTab.txt.gz 2017-09-11 02:52 61K
mmBlastTab.txt.gz 2022-07-12 17:09 61K
hgBlastTab.txt.gz 2022-07-12 17:02 60K
ensGtp.txt.gz 2021-05-25 14:46 59K
simpleRepeat.txt.gz 2011-10-06 16:18 54K
chrV_est.txt.gz 2012-05-28 14:19 52K
trackDb.txt.gz 2024-07-25 09:34 49K
chrXI_est.txt.gz 2012-05-28 14:19 49K
chrX_est.txt.gz 2012-05-28 14:19 49K
chrXIV_est.txt.gz 2012-05-28 14:19 46K
all_mrna.txt.gz 2020-05-07 04:28 43K
rnBlastTab.txt.gz 2012-02-26 05:30 42K
sgdOther.txt.gz 2011-10-06 16:15 41K
esRegGeneToMotif.txt.gz 2011-10-06 16:18 38K
sgdToName.txt.gz 2011-10-06 16:18 36K
multiz7waySummary.txt.gz 2011-10-06 16:15 33K
chrVIII_est.txt.gz 2012-05-28 14:19 32K
chrIII_est.txt.gz 2012-05-28 14:19 32K
ensemblToGeneName.txt.gz 2021-05-25 14:46 31K
sgdToSwissProt.txt.gz 2011-10-06 16:18 31K
sgdIsoforms.txt.gz 2011-10-06 16:18 31K
ncbiRefSeqCds.txt.gz 2021-02-10 16:08 30K
chrVI_est.txt.gz 2012-05-28 14:19 30K
chrIX_est.txt.gz 2012-05-28 14:19 24K
crisprRanges.txt.gz 2016-11-06 09:28 22K
ensemblSource.txt.gz 2021-05-25 14:46 22K
esRegUpstreamRegion.txt.gz 2011-10-06 16:18 19K
mrnaOrientInfo.txt.gz 2020-05-07 04:28 19K
esRegMotif.txt.gz 2011-10-06 16:15 17K
sgdClone.txt.gz 2011-10-06 16:18 16K
sgdOtherDescription.txt.gz 2011-10-06 16:17 12K
chrIV_intronEst.txt.gz 2012-05-28 14:19 12K
chrI_est.txt.gz 2012-05-28 14:19 11K
chrII_intronEst.txt.gz 2011-10-06 16:17 9.4K
esRegGeneToModule.txt.gz 2011-10-06 16:18 9.1K
chrVII_intronEst.txt.gz 2011-10-06 16:18 8.4K
tableDescriptions.txt.gz 2024-11-23 02:03 7.6K
tableList.txt.gz 2024-11-24 03:28 6.9K
chrXVI_intronEst.txt.gz 2012-05-28 14:19 6.6K
transRegCodeMotif.txt.gz 2011-10-06 16:18 6.5K
chrXII_intronEst.txt.gz 2012-05-28 14:19 5.7K
chrXIII_intronEst.txt.gz 2011-10-06 16:18 5.6K
chrIV_mrna.txt.gz 2020-05-07 04:20 5.5K
chrXV_intronEst.txt.gz 2011-10-06 16:15 5.3K
chrXII_mrna.txt.gz 2020-05-07 04:20 4.7K
chrVII_mrna.txt.gz 2020-05-07 04:25 4.4K
chrVIII_intronEst.txt.gz 2011-10-06 16:17 3.7K
chrX_mrna.txt.gz 2020-05-07 04:25 3.4K
chrV_intronEst.txt.gz 2011-10-06 16:15 3.4K
chrXIII_mrna.txt.gz 2020-05-07 04:20 3.3K
chrX_intronEst.txt.gz 2012-05-28 14:19 3.3K
chrXI_intronEst.txt.gz 2011-10-06 16:18 3.2K
chrXV_mrna.txt.gz 2020-05-07 04:20 3.2K
chrXVI_mrna.txt.gz 2020-05-07 04:20 3.1K
chrII_mrna.txt.gz 2020-05-07 04:20 3.0K
chrVI_intronEst.txt.gz 2012-05-28 14:19 3.0K
chrXIV_mrna.txt.gz 2020-05-07 04:20 2.8K
chrV_mrna.txt.gz 2020-05-07 04:21 2.6K
chrIX_intronEst.txt.gz 2011-10-06 16:15 2.6K
chrXIV_intronEst.txt.gz 2011-10-06 16:17 2.5K
chrXI_mrna.txt.gz 2020-05-07 04:20 2.3K
xenoRefSeqAli.sql 2020-08-20 09:46 2.1K
ncbiRefSeqPsl.sql 2021-02-10 15:45 2.1K
all_mrna.sql 2020-05-07 04:28 2.1K
chrXIII_mrna.sql 2020-05-07 04:20 2.1K
chrVIII_mrna.sql 2020-05-07 04:20 2.1K
chrXVI_mrna.sql 2020-05-07 04:20 2.1K
chrXIV_mrna.sql 2020-05-07 04:20 2.1K
chrXII_mrna.sql 2020-05-07 04:20 2.1K
chrVII_mrna.sql 2020-05-07 04:25 2.1K
chrIII_mrna.sql 2020-05-07 04:20 2.1K
chrXV_mrna.sql 2020-05-07 04:20 2.1K
chrXI_mrna.sql 2020-05-07 04:20 2.1K
chrVI_mrna.sql 2020-05-07 04:20 2.1K
chrIX_mrna.sql 2020-05-07 04:20 2.1K
chrIV_mrna.sql 2020-05-07 04:20 2.1K
chrII_mrna.sql 2020-05-07 04:20 2.1K
chrX_mrna.sql 2020-05-07 04:25 2.1K
chrV_mrna.sql 2020-05-07 04:21 2.1K
chrM_mrna.sql 2020-05-07 04:20 2.1K
chrI_mrna.sql 2020-05-07 04:20 2.1K
pslChainAWRI1631.sql 2011-10-06 16:15 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
chrXIII_intronEst.sql 2011-10-06 16:18 2.1K
chrVIII_intronEst.sql 2011-10-06 16:17 2.1K
chrXVI_intronEst.sql 2012-05-28 14:19 2.1K
chrXIV_intronEst.sql 2011-10-06 16:17 2.1K
chrXII_intronEst.sql 2012-05-28 14:19 2.1K
chrVII_intronEst.sql 2011-10-06 16:18 2.1K
chrIII_intronEst.sql 2011-10-06 16:18 2.1K
blastHg18KG.sql 2011-10-06 16:15 2.1K
chrXV_intronEst.sql 2011-10-06 16:15 2.1K
chrXI_intronEst.sql 2011-10-06 16:18 2.1K
chrVI_intronEst.sql 2012-05-28 14:19 2.1K
chrIX_intronEst.sql 2011-10-06 16:15 2.1K
chrIV_intronEst.sql 2012-05-28 14:19 2.1K
chrII_intronEst.sql 2011-10-06 16:17 2.1K
chrX_intronEst.sql 2012-05-28 14:19 2.0K
chrV_intronEst.sql 2011-10-06 16:15 2.0K
chrM_intronEst.sql 2011-10-06 16:17 2.0K
chrI_intronEst.sql 2011-10-06 16:18 2.0K
all_est.sql 2012-05-28 14:19 2.0K
chrXIII_est.sql 2012-05-28 14:19 2.0K
chrVIII_est.sql 2012-05-28 14:19 2.0K
chrXVI_est.sql 2012-05-28 14:19 2.0K
chrXIV_est.sql 2012-05-28 14:19 2.0K
chrXII_est.sql 2012-05-28 14:19 2.0K
chrVII_est.sql 2012-05-28 14:19 2.0K
chrIII_est.sql 2012-05-28 14:19 2.0K
chrXV_est.sql 2012-05-28 14:19 2.0K
chrXI_est.sql 2012-05-28 14:19 2.0K
chrVI_est.sql 2012-05-28 14:19 2.0K
chrIX_est.sql 2012-05-28 14:19 2.0K
chrIV_est.sql 2012-05-28 14:19 2.0K
chrII_est.sql 2012-05-28 14:19 2.0K
ncbiRefSeqLink.sql 2021-02-10 15:45 2.0K
chrX_est.sql 2012-05-28 14:19 2.0K
chrV_est.sql 2012-05-28 14:19 2.0K
chrM_est.sql 2011-10-06 16:16 2.0K
chrI_est.sql 2012-05-28 14:19 2.0K
ncbiRefSeqCurated.sql 2021-02-10 15:45 2.0K
xenoRefGene.sql 2020-08-20 09:46 2.0K
ncbiRefSeq.sql 2021-02-10 15:45 2.0K
ensGene.sql 2021-05-25 14:46 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
history.txt.gz 2014-10-19 15:03 1.9K
simpleRepeat.sql 2011-10-06 16:18 1.9K
mrnaOrientInfo.sql 2020-05-07 04:28 1.8K
chrVIII_mrna.txt.gz 2020-05-07 04:20 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
xenoRefFlat.sql 2020-08-20 09:46 1.7K
mmBlastTab.sql 2022-07-12 17:09 1.7K
hgBlastTab.sql 2022-07-12 17:02 1.7K
phastCons7way.sql 2011-10-06 16:15 1.7K
estOrientInfo.sql 2012-05-28 14:19 1.7K
drBlastTab.sql 2017-09-11 02:52 1.7K
sgdGene.sql 2011-10-06 16:18 1.7K
multiz7wayFrames.sql 2011-10-06 16:18 1.7K
esRegGeneToMotif.sql 2011-10-06 16:18 1.6K
sgdBlastTab.sql 2011-10-06 16:15 1.6K
rnBlastTab.sql 2012-02-26 05:30 1.6K
dmBlastTab.sql 2011-10-06 16:17 1.6K
ceBlastTab.sql 2011-10-06 16:15 1.6K
gbLoaded.sql 2020-08-20 09:58 1.6K
gold.sql 2011-10-06 16:17 1.6K
history.sql 2014-10-19 15:03 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:08 1.6K
esRegUpstreamRegion.sql 2011-10-06 16:18 1.6K
tableList.sql 2024-11-24 03:28 1.6K
chrIX_mrna.txt.gz 2020-05-07 04:20 1.5K
transRegCodeProbe.sql 2011-10-06 16:15 1.5K
transRegCode.sql 2011-10-06 16:15 1.5K
gap.sql 2011-10-06 16:17 1.5K
oreganno.sql 2016-05-15 11:29 1.5K
multiz7waySummary.sql 2011-10-06 16:15 1.5K
sgdCanonical.sql 2011-10-06 16:18 1.5K
phastConsElements7way.sql 2011-10-06 16:15 1.5K
locusName.sql 2016-11-06 09:28 1.5K
microsat.sql 2015-08-24 01:24 1.5K
chrIII_intronEst.txt.gz 2011-10-06 16:18 1.5K
sgdOther.sql 2011-10-06 16:15 1.5K
multiz7way.sql 2011-10-06 16:15 1.5K
extNcbiRefSeq.sql 2021-02-10 16:08 1.5K
sgdClone.sql 2011-10-06 16:18 1.5K
ensGtp.sql 2021-05-25 14:46 1.4K
crisprRanges.sql 2016-11-06 09:28 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
chromAlias.sql 2018-08-05 09:15 1.4K
transRegCodeMotif.sql 2011-10-06 16:18 1.4K
oregannoLink.sql 2016-05-15 11:29 1.4K
esRegMotif.sql 2011-10-06 16:15 1.4K
ensemblToGeneName.sql 2021-05-25 14:46 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:08 1.4K
bigFiles.sql 2024-11-24 03:28 1.4K
oregannoAttr.sql 2016-05-15 11:29 1.4K
ensemblSource.sql 2021-05-25 14:46 1.4K
growthCondition.sql 2014-10-19 15:03 1.4K
ncbiRefSeqCds.sql 2021-02-10 16:08 1.4K
transRegCodeCondition.sql 2011-10-06 16:18 1.4K
extFile.sql 2011-10-06 16:17 1.4K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2021-05-25 14:46 1.3K
esRegGeneToModule.sql 2011-10-06 16:18 1.3K
sgdIsoforms.sql 2011-10-06 16:18 1.3K
sgdOtherDescription.sql 2011-10-06 16:17 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:07 1.3K
choExpDistance.sql 2011-10-06 16:16 1.3K
sgdDescription.sql 2011-10-06 16:17 1.3K
chromInfo.sql 2011-10-06 16:17 1.3K
sgdToSwissProt.sql 2011-10-06 16:18 1.3K
crisprTargets.sql 2016-11-06 09:28 1.3K
sgdToName.sql 2011-10-06 16:18 1.3K
sgdPep.sql 2011-10-06 16:15 1.3K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
transRegCodeCondition.txt.gz 2011-10-06 16:18 1.2K
gc5BaseBw.sql 2011-10-06 16:17 1.2K
chrIII_mrna.txt.gz 2020-05-07 04:20 1.1K
chrI_intronEst.txt.gz 2011-10-06 16:18 1.1K
chrVI_mrna.txt.gz 2020-05-07 04:20 1.1K
chrM_mrna.txt.gz 2020-05-07 04:20 863
chrI_mrna.txt.gz 2020-05-07 04:20 845
growthCondition.txt.gz 2014-10-19 15:03 685
microsat.txt.gz 2015-08-24 01:24 345
chromAlias.txt.gz 2018-08-05 09:15 338
gold.txt.gz 2011-10-06 16:17 287
extFile.txt.gz 2011-10-06 16:17 265
grp.txt.gz 2014-03-02 04:14 199
chromInfo.txt.gz 2011-10-06 16:17 193
bigFiles.txt.gz 2024-11-24 03:28 114
extNcbiRefSeq.txt.gz 2021-02-10 16:08 89
ncbiRefSeqOther.txt.gz 2021-02-10 16:07 75
gc5BaseBw.txt.gz 2011-10-06 16:17 63
crisprTargets.txt.gz 2016-11-06 09:28 63
chrM_intronEst.txt.gz 2011-10-06 16:17 39
chrM_est.txt.gz 2011-10-06 16:16 33
gap.txt.gz 2011-10-06 16:17 28