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.
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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;'
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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.
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Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2012-06-11 07:51 63
bigFiles.txt.gz 2024-12-08 03:34 68
grp.txt.gz 2014-03-02 03:41 209
history.txt.gz 2012-06-11 06:20 392
snp138ExceptionDesc.txt.gz 2014-03-09 08:45 1.0K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
gc5BaseBw.sql 2012-06-11 07:51 1.2K
chromInfo.sql 2012-06-11 06:21 1.3K
ensPep.sql 2015-09-14 02:15 1.3K
snp138Seq.sql 2014-03-09 08:45 1.3K
grp.sql 2014-03-02 03:41 1.3K
ensemblSource.sql 2015-09-14 02:15 1.4K
ucscToEnsembl.sql 2013-06-16 17:56 1.4K
snp138ExceptionDesc.sql 2014-03-09 08:45 1.4K
ensemblToGeneName.sql 2015-09-14 02:15 1.4K
bigFiles.sql 2024-12-08 03:34 1.4K
chromAlias.sql 2018-02-18 06:35 1.4K
ucscToINSDC.sql 2013-09-15 13:24 1.4K
ucscToRefSeq.sql 2018-02-18 06:35 1.4K
ensGtp.sql 2015-09-14 02:14 1.4K
windowmaskerSdust.sql 2012-06-11 06:58 1.4K
tableDescriptions.sql 2024-12-07 02:03 1.5K
chainMm10Link.sql 2012-06-11 07:47 1.5K
microsat.sql 2015-08-23 17:01 1.5K
animalQtl.sql 2014-06-29 20:27 1.5K
genscanSubopt.sql 2012-06-11 06:20 1.5K
history.sql 2012-06-11 06:20 1.5K
cytoBandIdeo.sql 2013-04-28 15:31 1.5K
gap.sql 2012-06-11 07:11 1.5K
chainTaeGut2Link.sql 2014-05-18 18:43 1.5K
chainGeoFor1Link.sql 2012-08-19 12:01 1.6K
chainPetMar2Link.sql 2013-01-24 00:12 1.6K
tableList.sql 2024-12-08 03:34 1.6K
gold.sql 2012-06-11 06:20 1.6K
gbLoaded.sql 2020-08-21 21:13 1.6K
genscan.sql 2012-06-11 06:20 1.6K
cpgIslandExt.sql 2012-06-11 06:23 1.6K
chainMm10.sql 2012-06-11 07:27 1.6K
chainTaeGut2.sql 2014-05-18 18:43 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K
chainGeoFor1.sql 2012-08-19 12:04 1.7K
chainPetMar2.sql 2013-01-24 00:12 1.7K
refFlat.sql 2020-08-21 20:38 1.7K
snp138CodingDbSnp.sql 2014-03-09 08:45 1.7K
xenoRefFlat.sql 2020-08-21 20:43 1.7K
hgFindSpec.sql 2024-07-25 09:34 1.8K
rmsk.sql 2012-06-11 07:45 1.8K
estOrientInfo.sql 2020-05-08 00:49 1.8K
mrnaOrientInfo.sql 2020-08-21 20:43 1.8K
simpleRepeat.sql 2012-06-11 06:21 1.9K
nestedRepeats.sql 2012-06-11 07:25 1.9K
ensGene.sql 2015-09-14 02:15 1.9K
augustusGene.sql 2015-07-26 13:45 1.9K
refGene.sql 2020-08-21 20:38 1.9K
xenoRefGene.sql 2020-08-21 20:43 2.0K
netMm10.sql 2012-06-11 07:08 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netTaeGut2.sql 2014-05-18 18:44 2.1K
netGeoFor1.sql 2012-08-19 12:01 2.1K
netPetMar2.sql 2013-01-24 00:12 2.1K
all_est.sql 2020-05-08 00:49 2.1K
all_mrna.sql 2020-08-21 19:59 2.1K
xenoMrna.sql 2020-08-21 19:59 2.1K
intronEst.sql 2020-05-08 00:49 2.1K
refSeqAli.sql 2020-08-21 20:58 2.1K
xenoRefSeqAli.sql 2020-08-21 20:59 2.1K
pubsBingBlatPsl.sql 2014-01-26 12:58 2.2K
pubsBingBlat.sql 2014-01-26 12:58 2.4K
snp138.sql 2014-03-09 08:44 2.9K
snp138Mult.sql 2014-03-09 08:45 2.9K
snp138Common.sql 2014-03-09 08:45 3.0K
tableList.txt.gz 2024-12-08 03:34 4.4K
tableDescriptions.txt.gz 2024-12-07 02:03 7.8K
microsat.txt.gz 2015-08-23 17:01 24K
animalQtl.txt.gz 2014-06-29 20:27 33K
gbLoaded.txt.gz 2020-08-21 21:13 44K
ensemblSource.txt.gz 2015-09-14 02:15 56K
trackDb.txt.gz 2024-07-25 09:34 73K
chromInfo.txt.gz 2012-06-11 06:21 78K
cytoBandIdeo.txt.gz 2013-04-28 15:31 79K
ucscToEnsembl.txt.gz 2013-06-16 17:56 99K
ensemblToGeneName.txt.gz 2015-09-14 02:15 112K
ucscToINSDC.txt.gz 2013-09-15 13:24 120K
ucscToRefSeq.txt.gz 2018-02-18 06:35 132K
chromAlias.txt.gz 2018-02-18 06:35 178K
gap.txt.gz 2012-06-11 07:11 181K
ensGtp.txt.gz 2015-09-14 02:14 187K
gold.txt.gz 2012-06-11 06:20 213K
snp138Common.txt.gz 2014-03-09 08:45 383K
cpgIslandExt.txt.gz 2012-06-11 06:23 472K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K
mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K
refFlat.txt.gz 2020-08-21 20:38 663K
pubsBingBlatPsl.txt.gz 2014-01-26 12:58 664K
nestedRepeats.txt.gz 2012-06-11 07:25 671K
refGene.txt.gz 2020-08-21 20:38 711K
refSeqAli.txt.gz 2020-08-21 20:58 753K
pubsBingBlat.txt.gz 2014-01-26 12:58 844K
genscan.txt.gz 2012-06-11 06:20 1.4M
augustusGene.txt.gz 2015-07-26 13:45 1.5M
ensGene.txt.gz 2015-09-14 02:15 1.7M
all_mrna.txt.gz 2020-08-21 19:59 1.9M
netPetMar2.txt.gz 2013-01-24 00:12 2.3M
snp138CodingDbSnp.txt.gz 2014-03-09 08:45 2.3M
chainPetMar2.txt.gz 2013-01-24 00:12 2.8M
genscanSubopt.txt.gz 2012-06-11 06:21 2.8M
snp138Mult.txt.gz 2014-03-09 08:45 2.9M
simpleRepeat.txt.gz 2012-06-11 06:21 4.9M
ensPep.txt.gz 2015-09-14 02:15 5.2M
chainMm10.txt.gz 2012-06-11 07:27 7.2M
estOrientInfo.txt.gz 2020-05-08 00:49 7.2M
netMm10.txt.gz 2012-06-11 07:09 7.7M
chainPetMar2Link.txt.gz 2013-01-24 00:12 12M
rmsk.txt.gz 2012-06-11 07:45 14M
chainTaeGut2.txt.gz 2014-05-18 18:43 18M
xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M
intronEst.txt.gz 2020-05-08 00:49 19M
xenoRefFlat.txt.gz 2020-08-21 20:43 20M
xenoRefGene.txt.gz 2020-08-21 20:43 22M
netTaeGut2.txt.gz 2014-05-18 18:44 31M
netGeoFor1.txt.gz 2012-08-19 12:01 35M
all_est.txt.gz 2020-05-08 00:49 36M
chainMm10Link.txt.gz 2012-06-11 07:48 53M
windowmaskerSdust.txt.gz 2012-06-11 06:59 54M
snp138Seq.txt.gz 2014-03-09 08:45 57M
chainGeoFor1.txt.gz 2012-08-19 12:04 93M
snp138.txt.gz 2014-03-09 08:44 133M
xenoMrna.txt.gz 2020-08-21 19:59 173M
chainTaeGut2Link.txt.gz 2014-05-18 18:43 222M
chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M