This directory contains a dump of the UCSC genome annotation database for
the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2))
from the Chicken Genome Sequencing Consortium.
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/111
http://www.ncbi.nlm.nih.gov/genome/assembly/317958
http://www.ncbi.nlm.nih.gov/bioproject/13342
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=galGal4
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/galGal4/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/galGal4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/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 galGal4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galGal4 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
------------------------------------------------------------------
The Chicken sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
if the providers of these data are properly cited:
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide unique
perspectives on vertebrate evolution.
Nature. 2004 Dec 9;432(7018):695-716. PMID: 15592404
See http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. Any redistribution of the data should carry this notice.
All the files and tables in this directory are freely usable for any purpose.
------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
history.sql 2012-06-11 06:20 1.5K
history.txt.gz 2012-06-11 06:20 392
genscan.sql 2012-06-11 06:20 1.6K
genscan.txt.gz 2012-06-11 06:20 1.4M
gold.sql 2012-06-11 06:20 1.6K
gold.txt.gz 2012-06-11 06:20 213K
genscanSubopt.sql 2012-06-11 06:20 1.5K
genscanSubopt.txt.gz 2012-06-11 06:21 2.8M
chromInfo.sql 2012-06-11 06:21 1.3K
chromInfo.txt.gz 2012-06-11 06:21 78K
simpleRepeat.sql 2012-06-11 06:21 1.9K
simpleRepeat.txt.gz 2012-06-11 06:21 4.9M
cpgIslandExt.sql 2012-06-11 06:23 1.6K
cpgIslandExt.txt.gz 2012-06-11 06:23 472K
windowmaskerSdust.sql 2012-06-11 06:58 1.4K
windowmaskerSdust.txt.gz 2012-06-11 06:59 54M
netMm10.sql 2012-06-11 07:08 2.0K
netMm10.txt.gz 2012-06-11 07:09 7.7M
gap.sql 2012-06-11 07:11 1.5K
gap.txt.gz 2012-06-11 07:11 181K
nestedRepeats.sql 2012-06-11 07:25 1.9K
nestedRepeats.txt.gz 2012-06-11 07:25 671K
chainMm10.sql 2012-06-11 07:27 1.6K
chainMm10.txt.gz 2012-06-11 07:27 7.2M
rmsk.sql 2012-06-11 07:45 1.8K
rmsk.txt.gz 2012-06-11 07:45 14M
chainMm10Link.sql 2012-06-11 07:47 1.5K
chainMm10Link.txt.gz 2012-06-11 07:48 53M
gc5BaseBw.sql 2012-06-11 07:51 1.2K
gc5BaseBw.txt.gz 2012-06-11 07:51 63
netGeoFor1.sql 2012-08-19 12:01 2.1K
netGeoFor1.txt.gz 2012-08-19 12:01 35M
chainGeoFor1Link.sql 2012-08-19 12:01 1.6K
chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M
chainGeoFor1.sql 2012-08-19 12:04 1.7K
chainGeoFor1.txt.gz 2012-08-19 12:04 93M
chainPetMar2Link.sql 2013-01-24 00:12 1.6K
chainPetMar2Link.txt.gz 2013-01-24 00:12 12M
netPetMar2.sql 2013-01-24 00:12 2.1K
chainPetMar2.sql 2013-01-24 00:12 1.7K
chainPetMar2.txt.gz 2013-01-24 00:12 2.8M
netPetMar2.txt.gz 2013-01-24 00:12 2.3M
cytoBandIdeo.sql 2013-04-28 15:31 1.5K
cytoBandIdeo.txt.gz 2013-04-28 15:31 79K
ucscToEnsembl.sql 2013-06-16 17:56 1.4K
ucscToEnsembl.txt.gz 2013-06-16 17:56 99K
ucscToINSDC.sql 2013-09-15 13:24 1.4K
ucscToINSDC.txt.gz 2013-09-15 13:24 120K
pubsBingBlat.sql 2014-01-26 12:58 2.4K
pubsBingBlat.txt.gz 2014-01-26 12:58 844K
pubsBingBlatPsl.sql 2014-01-26 12:58 2.2K
pubsBingBlatPsl.txt.gz 2014-01-26 12:58 664K
grp.sql 2014-03-02 03:41 1.3K
grp.txt.gz 2014-03-02 03:41 209
snp138.sql 2014-03-09 08:44 2.9K
snp138.txt.gz 2014-03-09 08:44 133M
snp138CodingDbSnp.sql 2014-03-09 08:45 1.7K
snp138CodingDbSnp.txt.gz 2014-03-09 08:45 2.3M
snp138Common.sql 2014-03-09 08:45 3.0K
snp138Common.txt.gz 2014-03-09 08:45 383K
snp138ExceptionDesc.sql 2014-03-09 08:45 1.4K
snp138ExceptionDesc.txt.gz 2014-03-09 08:45 1.0K
snp138Mult.sql 2014-03-09 08:45 2.9K
snp138Mult.txt.gz 2014-03-09 08:45 2.9M
snp138Seq.sql 2014-03-09 08:45 1.3K
snp138Seq.txt.gz 2014-03-09 08:45 57M
chainTaeGut2.sql 2014-05-18 18:43 1.7K
chainTaeGut2.txt.gz 2014-05-18 18:43 18M
chainTaeGut2Link.sql 2014-05-18 18:43 1.5K
chainTaeGut2Link.txt.gz 2014-05-18 18:43 222M
netTaeGut2.sql 2014-05-18 18:44 2.1K
netTaeGut2.txt.gz 2014-05-18 18:44 31M
cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K
animalQtl.sql 2014-06-29 20:27 1.5K
animalQtl.txt.gz 2014-06-29 20:27 33K
augustusGene.sql 2015-07-26 13:45 1.9K
augustusGene.txt.gz 2015-07-26 13:45 1.5M
microsat.sql 2015-08-23 17:01 1.5K
microsat.txt.gz 2015-08-23 17:01 24K
ensGtp.sql 2015-09-14 02:14 1.4K
ensGtp.txt.gz 2015-09-14 02:14 187K
ensPep.sql 2015-09-14 02:15 1.3K
ensPep.txt.gz 2015-09-14 02:15 5.2M
ensemblSource.sql 2015-09-14 02:15 1.4K
ensemblSource.txt.gz 2015-09-14 02:15 56K
ensemblToGeneName.sql 2015-09-14 02:15 1.4K
ensemblToGeneName.txt.gz 2015-09-14 02:15 112K
ensGene.sql 2015-09-14 02:15 1.9K
ensGene.txt.gz 2015-09-14 02:15 1.7M
chromAlias.sql 2018-02-18 06:35 1.4K
chromAlias.txt.gz 2018-02-18 06:35 178K
ucscToRefSeq.sql 2018-02-18 06:35 1.4K
ucscToRefSeq.txt.gz 2018-02-18 06:35 132K
estOrientInfo.sql 2020-05-08 00:49 1.8K
estOrientInfo.txt.gz 2020-05-08 00:49 7.2M
intronEst.sql 2020-05-08 00:49 2.1K
intronEst.txt.gz 2020-05-08 00:49 19M
all_est.sql 2020-05-08 00:49 2.1K
all_est.txt.gz 2020-05-08 00:49 36M
all_mrna.sql 2020-08-21 19:59 2.1K
all_mrna.txt.gz 2020-08-21 19:59 1.9M
xenoMrna.sql 2020-08-21 19:59 2.1K
xenoMrna.txt.gz 2020-08-21 19:59 173M
refGene.sql 2020-08-21 20:38 1.9K
refGene.txt.gz 2020-08-21 20:38 711K
refFlat.sql 2020-08-21 20:38 1.7K
refFlat.txt.gz 2020-08-21 20:38 663K
xenoRefGene.sql 2020-08-21 20:43 2.0K
xenoRefGene.txt.gz 2020-08-21 20:43 22M
xenoRefFlat.sql 2020-08-21 20:43 1.7K
xenoRefFlat.txt.gz 2020-08-21 20:43 20M
mrnaOrientInfo.sql 2020-08-21 20:43 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K
refSeqAli.sql 2020-08-21 20:58 2.1K
refSeqAli.txt.gz 2020-08-21 20:58 753K
xenoRefSeqAli.sql 2020-08-21 20:59 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M
gbLoaded.sql 2020-08-21 21:13 1.6K
gbLoaded.txt.gz 2020-08-21 21:13 44K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 73K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
tableDescriptions.sql 2024-12-28 02:05 1.5K
tableDescriptions.txt.gz 2024-12-28 02:05 7.8K
tableList.sql 2024-12-29 03:31 1.6K
tableList.txt.gz 2024-12-29 03:31 4.4K
bigFiles.sql 2024-12-29 03:31 1.4K
bigFiles.txt.gz 2024-12-29 03:31 68