This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of the chimp genome
(panTro3, CGSC 2.1.3 (GCA_000001515.3)) from the
Chimp Genome Sequencing Consortium. The annotations were generated
by UCSC and collaborators worldwide.
This assembly was produced by the Chimpanzee Sequencing and Analysis Consortium.
For more information on the chimp genome, see the project website:
http://genome.wustl.edu/genomes/view/pan_troglodytes/
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=panTro3
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/panTro3/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/panTro3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/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 panTro3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
##############################################################################
The chimpanzee sequence is made freely available before scientific
publication with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged
in databases.
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the providers of these data are
properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
gold.sql 2011-02-25 17:09 1.6K
gold.txt.gz 2011-02-25 17:09 3.0M
chromInfo.sql 2011-02-25 17:10 1.3K
chromInfo.txt.gz 2011-02-25 17:10 138K
nestedRepeats.sql 2011-02-25 17:10 1.9K
nestedRepeats.txt.gz 2011-02-25 17:10 18M
ctgPos2.sql 2011-02-25 17:10 1.5K
ctgPos2.txt.gz 2011-02-25 17:10 2.5M
history.sql 2011-02-25 17:11 1.5K
history.txt.gz 2011-02-25 17:11 147
chainHg19.sql 2011-02-25 17:11 1.6K
chainHg19.txt.gz 2011-02-25 17:11 28M
simpleRepeat.sql 2011-02-25 17:13 1.9K
simpleRepeat.txt.gz 2011-02-25 17:13 26M
cpgIslandExt.sql 2011-02-25 17:14 1.6K
cpgIslandExt.txt.gz 2011-02-25 17:14 627K
netHg19.sql 2011-02-25 17:17 2.0K
netHg19.txt.gz 2011-02-25 17:18 10M
chainHg19Link.sql 2011-02-25 17:18 1.5K
chainHg19Link.txt.gz 2011-02-25 17:19 124M
gap.sql 2011-02-25 17:24 1.5K
gap.txt.gz 2011-02-25 17:24 2.3M
rmsk.sql 2011-02-25 17:28 1.8K
rmsk.txt.gz 2011-02-25 17:29 137M
gc5BaseBw.sql 2011-02-25 17:35 1.2K
gc5BaseBw.txt.gz 2011-02-25 17:35 63
chainDanRer7.sql 2011-03-15 09:00 1.6K
chainDanRer7.txt.gz 2011-03-15 09:02 160M
chainDanRer7Link.sql 2011-03-15 09:08 1.5K
chainDanRer7Link.txt.gz 2011-03-15 09:15 524M
netDanRer7.sql 2011-03-15 09:36 2.0K
netDanRer7.txt.gz 2011-03-15 09:36 8.1M
chainGalGal3Link.sql 2011-05-03 13:23 1.5K
chainGalGal3Link.txt.gz 2011-05-03 13:25 114M
chainPonAbe2.sql 2011-05-03 13:29 1.6K
chainPonAbe2.txt.gz 2011-05-03 13:29 26M
chainPonAbe2Link.sql 2011-05-03 13:30 1.5K
chainPonAbe2Link.txt.gz 2011-05-03 13:32 175M
netEquCab2.sql 2011-05-03 13:39 2.0K
netEquCab2.txt.gz 2011-05-03 13:41 70M
chainGalGal3.sql 2011-05-03 13:43 1.6K
chainGalGal3.txt.gz 2011-05-03 13:44 21M
netGalGal3.sql 2011-05-03 13:44 2.0K
netGalGal3.txt.gz 2011-05-03 13:45 12M
chainEquCab2Link.sql 2011-05-03 13:45 1.5K
chainEquCab2Link.txt.gz 2011-05-03 13:59 1.0G
chainEquCab2.sql 2011-05-03 14:38 1.6K
chainEquCab2.txt.gz 2011-05-03 14:41 258M
netPonAbe2.sql 2011-05-03 14:49 2.0K
netPonAbe2.txt.gz 2011-05-03 14:50 20M
chainMm9Link.sql 2011-05-24 00:21 1.5K
chainMm9Link.txt.gz 2011-05-24 00:24 520M
netRheMac2.sql 2011-05-24 00:30 2.0K
netRheMac2.txt.gz 2011-05-24 00:30 26M
netMm9.sql 2011-05-24 00:31 2.0K
netMm9.txt.gz 2011-05-24 00:32 73M
netCalJac3.sql 2011-05-24 00:32 2.0K
netCalJac3.txt.gz 2011-05-24 00:33 45M
chainMm9.sql 2011-05-24 00:34 1.6K
chainMm9.txt.gz 2011-05-24 00:34 67M
chainCalJac3.sql 2011-05-24 00:35 1.6K
chainCalJac3.txt.gz 2011-05-24 00:35 15M
chainCalJac3Link.sql 2011-05-24 00:35 1.5K
chainCalJac3Link.txt.gz 2011-05-24 00:37 235M
chainRheMac2.sql 2011-05-24 00:40 1.6K
chainRheMac2.txt.gz 2011-05-24 00:40 11M
chainRheMac2Link.sql 2011-05-24 00:40 1.5K
chainRheMac2Link.txt.gz 2011-05-24 00:41 162M
chainCanFam2Link.sql 2011-05-30 01:12 1.5K
chainCanFam2Link.txt.gz 2011-05-30 01:13 524M
chainCanFam2.sql 2011-05-30 01:18 1.6K
chainCanFam2.txt.gz 2011-05-30 01:19 43M
netCanFam2.sql 2011-05-30 01:19 2.0K
netCanFam2.txt.gz 2011-05-30 01:20 77M
nscanGene.sql 2011-06-26 14:55 1.9K
nscanGene.txt.gz 2011-06-26 14:55 2.2M
nscanPep.sql 2011-06-26 14:55 1.3K
nscanPep.txt.gz 2011-06-26 14:55 6.1M
phyloP12wayPrimate.sql 2011-08-21 03:56 1.7K
phyloP12wayPrimate.txt.gz 2011-08-21 03:56 82M
phastConsElements12way.sql 2011-08-21 03:56 1.5K
phastConsElements12way.txt.gz 2011-08-21 03:56 14M
phastCons12wayPrimate.sql 2011-08-21 03:56 1.7K
phastCons12wayPrimate.txt.gz 2011-08-21 03:57 80M
multiz12waySummary.sql 2011-08-21 03:57 1.5K
multiz12waySummary.txt.gz 2011-08-21 03:57 23M
multiz12wayFrames.sql 2011-08-21 03:57 1.7K
multiz12wayFrames.txt.gz 2011-08-21 03:57 17M
phastConsElements12wayPrimate.sql 2011-08-21 03:57 1.5K
multiz12way.sql 2011-08-21 03:57 1.5K
phastConsElements12wayPrimate.txt.gz 2011-08-21 03:57 3.2M
multiz12way.txt.gz 2011-08-21 03:58 209M
extFile.sql 2011-08-21 03:59 1.4K
extFile.txt.gz 2011-08-21 03:59 81
phastCons12way.sql 2011-08-21 03:59 1.7K
phastCons12way.txt.gz 2011-08-21 03:59 77M
phyloP12way.sql 2011-08-21 03:59 1.7K
phyloP12way.txt.gz 2011-08-21 04:00 86M
chainMonDom5Link.sql 2011-11-14 03:05 1.5K
chainMonDom5Link.txt.gz 2011-11-14 03:09 1.2G
netMonDom5.sql 2011-11-14 03:18 2.0K
netMonDom5.txt.gz 2011-11-14 03:18 31M
chainMonDom5.sql 2011-11-14 03:18 1.6K
chainMonDom5.txt.gz 2011-11-14 03:19 341M
netGorGor3.sql 2011-11-27 14:04 2.0K
netGorGor3.txt.gz 2011-11-27 14:04 16M
chainGorGor3Link.sql 2011-11-27 14:04 1.5K
chainGorGor3Link.txt.gz 2011-11-27 14:04 108M
chainGorGor3.sql 2011-11-27 14:05 1.6K
chainGorGor3.txt.gz 2011-11-27 14:05 28M
tRNAs.sql 2012-04-23 09:16 1.7K
tRNAs.txt.gz 2012-04-23 09:16 12K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 234
cpgIslandExtUnmasked.sql 2014-06-01 18:26 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:26 1.0M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
microsat.sql 2015-08-23 23:47 1.5K
microsat.txt.gz 2015-08-23 23:47 349K
all_est.sql 2016-07-17 10:50 2.1K
all_est.txt.gz 2016-07-17 10:50 875K
estOrientInfo.sql 2016-07-17 10:52 1.8K
estOrientInfo.txt.gz 2016-07-17 10:52 221K
intronEst.sql 2016-07-17 10:52 2.1K
intronEst.txt.gz 2016-07-17 10:52 677K
chromAlias.sql 2016-09-15 18:01 1.4K
chromAlias.txt.gz 2016-09-15 18:01 134K
all_mrna.sql 2020-05-08 18:29 2.1K
all_mrna.txt.gz 2020-05-08 18:29 302K
xenoMrna.sql 2020-08-22 18:48 2.1K
xenoMrna.txt.gz 2020-08-22 18:48 321M
refGene.sql 2020-08-22 18:57 1.9K
refGene.txt.gz 2020-08-22 18:57 217K
refFlat.sql 2020-08-22 18:57 1.7K
refFlat.txt.gz 2020-08-22 18:57 200K
xenoRefGene.sql 2020-08-22 18:57 2.0K
xenoRefGene.txt.gz 2020-08-22 18:57 33M
xenoRefFlat.sql 2020-08-22 19:12 1.7K
xenoRefFlat.txt.gz 2020-08-22 19:12 30M
mrnaOrientInfo.sql 2020-08-22 19:12 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 19:12 109K
refSeqAli.sql 2020-08-22 19:12 2.1K
refSeqAli.txt.gz 2020-08-22 19:12 224K
xenoRefSeqAli.sql 2020-08-22 19:12 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 19:12 31M
gbLoaded.sql 2020-08-22 19:12 1.6K
gbLoaded.txt.gz 2020-08-22 19:12 41K
trackDb.sql 2023-03-28 13:52 2.1K
trackDb.txt.gz 2023-03-28 13:52 46K
hgFindSpec.sql 2023-03-28 13:52 1.8K
hgFindSpec.txt.gz 2023-03-28 13:52 637
tableDescriptions.sql 2024-11-23 02:03 1.4K
tableDescriptions.txt.gz 2024-11-23 02:03 7.1K
tableList.sql 2024-11-24 03:28 1.6K
tableList.txt.gz 2024-11-24 03:28 4.5K
bigFiles.sql 2024-11-24 03:28 1.4K
bigFiles.txt.gz 2024-11-24 03:28 68