This directory contains a dump of the UCSC genome annotation database for the
Dec 2015 (Gallus_gallus-5.0/galGal5) assembly of the chicken genome
(galGal5, International Chicken Genome Consortium)
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/595851
http://www.ncbi.nlm.nih.gov/bioproject/10808
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=galGal5
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/galGal5/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/galGal5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal5/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 galGal5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galGal5 --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 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.
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
all_est.sql 2020-05-08 00:49 2.1K
all_est.txt.gz 2020-05-08 00:49 39M
all_mrna.sql 2020-08-21 19:59 2.1K
all_mrna.txt.gz 2020-08-21 19:59 2.0M
augustusGene.sql 2016-09-18 08:17 1.9K
augustusGene.txt.gz 2016-09-18 08:17 1.7M
bigFiles.sql 2024-11-17 03:15 1.4K
bigFiles.txt.gz 2024-11-17 03:15 120
chainAquChr2.sql 2018-04-01 06:28 1.7K
chainAquChr2.txt.gz 2018-04-01 06:28 72M
chainAquChr2Link.sql 2018-04-01 06:28 1.5K
chainAquChr2Link.txt.gz 2018-04-01 06:29 530M
chainDanRer10.sql 2016-09-18 08:17 1.7K
chainDanRer10.txt.gz 2016-09-18 08:17 12M
chainDanRer10Link.sql 2016-09-18 08:17 1.6K
chainDanRer10Link.txt.gz 2016-09-18 08:17 54M
chainHg38.sql 2016-09-18 08:17 1.7K
chainHg38.txt.gz 2016-09-18 08:17 27M
chainHg38Link.sql 2016-09-18 08:17 1.5K
chainHg38Link.txt.gz 2016-09-18 08:18 164M
chainMelGal5.sql 2017-03-19 21:14 1.7K
chainMelGal5.txt.gz 2017-03-19 21:16 309M
chainMelGal5Link.sql 2017-03-19 21:20 1.5K
chainMelGal5Link.txt.gz 2017-03-19 21:27 1.4G
chainMm10.sql 2016-09-18 08:18 1.7K
chainMm10.txt.gz 2016-09-18 08:18 8.9M
chainMm10Link.sql 2016-09-18 08:18 1.5K
chainMm10Link.txt.gz 2016-09-18 08:18 73M
chainRn6.sql 2016-09-18 08:19 1.7K
chainRn6.txt.gz 2016-09-18 08:19 14M
chainRn6Link.sql 2016-09-18 08:19 1.5K
chainRn6Link.txt.gz 2016-09-18 08:19 96M
chainXenTro9.sql 2017-12-14 10:29 1.7K
chainXenTro9.txt.gz 2017-12-14 10:29 6.8M
chainXenTro9Link.sql 2017-12-14 10:29 1.5K
chainXenTro9Link.txt.gz 2017-12-14 10:29 25M
chromAlias.sql 2017-09-03 05:25 1.4K
chromAlias.txt.gz 2017-09-03 05:25 261K
chromInfo.sql 2016-09-18 08:19 1.4K
chromInfo.txt.gz 2016-09-18 08:19 127K
cpgIslandExt.sql 2016-09-18 08:19 1.7K
cpgIslandExt.txt.gz 2016-09-18 08:19 536K
cpgIslandExtUnmasked.sql 2016-09-18 08:19 1.7K
cpgIslandExtUnmasked.txt.gz 2016-09-18 08:19 746K
cytoBandIdeo.sql 2016-09-18 08:19 1.5K
cytoBandIdeo.txt.gz 2016-09-18 08:19 116K
ensGene.sql 2018-08-05 06:42 1.9K
ensGene.txt.gz 2018-08-05 06:42 2.4M
ensGtp.sql 2018-08-05 06:42 1.4K
ensGtp.txt.gz 2018-08-05 06:42 387K
ensPep.sql 2018-08-05 06:42 1.3K
ensPep.txt.gz 2018-08-05 06:42 8.7M
ensemblSource.sql 2018-08-05 06:42 1.4K
ensemblSource.txt.gz 2018-08-05 06:42 121K
ensemblToGeneName.sql 2018-08-05 06:43 1.4K
ensemblToGeneName.txt.gz 2018-08-05 06:43 167K
estOrientInfo.sql 2020-05-08 00:49 1.8K
estOrientInfo.txt.gz 2020-05-08 00:49 8.0M
extNcbiRefSeq.sql 2018-02-09 14:16 1.5K
extNcbiRefSeq.txt.gz 2018-02-09 14:16 91
gap.sql 2016-09-18 08:19 1.6K
gap.txt.gz 2016-09-18 08:19 18K
gbLoaded.sql 2020-08-21 19:59 1.6K
gbLoaded.txt.gz 2020-08-21 19:59 44K
gc5BaseBw.sql 2016-09-18 08:19 1.3K
gc5BaseBw.txt.gz 2016-09-18 08:19 66
genscan.sql 2016-09-18 08:19 1.7K
genscan.txt.gz 2016-09-18 08:19 1.7M
gold.sql 2016-09-18 08:19 1.7K
gold.txt.gz 2016-09-18 08:19 286K
grcIncidentDb.sql 2018-05-13 05:42 1.3K
grcIncidentDb.txt.gz 2018-05-13 05:42 77
grp.sql 2016-09-18 08:19 1.3K
grp.txt.gz 2016-09-18 08:19 213
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.4K
history.sql 2016-09-18 08:19 1.6K
history.txt.gz 2016-09-18 08:19 816
intronEst.sql 2020-05-08 00:49 2.1K
intronEst.txt.gz 2020-05-08 00:49 21M
microsat.sql 2016-09-18 08:19 1.5K
microsat.txt.gz 2016-09-18 08:19 25K
mrnaOrientInfo.sql 2020-08-21 19:59 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 19:59 590K
ncbiRefSeq.sql 2018-02-09 13:42 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:42 3.0M
ncbiRefSeqCds.sql 2018-02-09 14:16 1.4K
ncbiRefSeqCds.txt.gz 2018-02-09 14:16 317K
ncbiRefSeqCurated.sql 2018-02-09 13:42 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:42 657K
ncbiRefSeqLink.sql 2018-02-09 13:42 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:42 1.6M
ncbiRefSeqOther.sql 2018-02-09 14:16 1.3K
ncbiRefSeqOther.txt.gz 2018-02-09 14:16 75
ncbiRefSeqPepTable.sql 2018-02-09 14:16 1.4K
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:16 9.2M
ncbiRefSeqPredicted.sql 2018-02-09 13:42 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:42 2.6M
ncbiRefSeqPsl.sql 2018-02-09 13:42 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:42 4.3M
nestedRepeats.sql 2016-09-18 08:19 1.9K
nestedRepeats.txt.gz 2016-09-18 08:19 1.5M
netAquChr2.sql 2018-04-01 06:31 2.1K
netAquChr2.txt.gz 2018-04-01 06:31 27M
netDanRer10.sql 2016-09-18 08:19 2.1K
netDanRer10.txt.gz 2016-09-18 08:19 5.6M
netHg38.sql 2016-09-18 08:19 2.1K
netHg38.txt.gz 2016-09-18 08:19 11M
netMelGal5.sql 2017-03-19 22:25 2.1K
netMelGal5.txt.gz 2017-03-19 22:25 21M
netMm10.sql 2016-09-18 08:19 2.1K
netMm10.txt.gz 2016-09-18 08:20 8.9M
netRn6.sql 2016-09-18 08:20 2.1K
netRn6.txt.gz 2016-09-18 08:20 9.1M
netXenTro9.sql 2017-12-14 10:29 2.1K
netXenTro9.txt.gz 2017-12-14 10:29 5.5M
refFlat.sql 2020-08-21 19:59 1.7K
refFlat.txt.gz 2020-08-21 19:59 676K
refGene.sql 2020-08-21 19:59 1.9K
refGene.txt.gz 2020-08-21 19:59 726K
refSeqAli.sql 2020-08-21 19:59 2.1K
refSeqAli.txt.gz 2020-08-21 19:59 755K
rmsk.sql 2016-09-18 08:20 1.9K
rmsk.txt.gz 2016-09-18 08:20 22M
seqNcbiRefSeq.sql 2018-02-09 14:16 1.6K
seqNcbiRefSeq.txt.gz 2018-02-09 14:16 871K
simpleRepeat.sql 2016-09-18 08:20 1.9K
simpleRepeat.txt.gz 2016-09-18 08:20 17M
snp147.sql 2017-04-02 18:42 3.0K
snp147.txt.gz 2017-04-02 18:52 332M
snp147CodingDbSnp.sql 2017-04-02 19:05 1.7K
snp147CodingDbSnp.txt.gz 2017-04-02 19:05 12M
snp147ExceptionDesc.sql 2017-04-02 19:06 1.4K
snp147ExceptionDesc.txt.gz 2017-04-02 19:06 1.0K
snp147Mult.sql 2017-04-02 19:06 3.0K
snp147Mult.txt.gz 2017-04-02 19:06 1.2M
snp147Seq.sql 2017-04-02 19:06 1.3K
snp147Seq.txt.gz 2017-04-02 19:07 128M
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 7.9K
tableList.sql 2024-11-17 03:15 1.6K
tableList.txt.gz 2024-11-17 03:15 4.9K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 103K
ucscToINSDC.sql 2016-09-18 08:20 1.4K
ucscToINSDC.txt.gz 2016-09-18 08:20 181K
ucscToRefSeq.sql 2016-09-18 08:20 1.4K
ucscToRefSeq.txt.gz 2016-09-18 08:20 180K
windowmaskerSdust.sql 2016-09-18 08:20 1.5K
windowmaskerSdust.txt.gz 2016-09-18 08:20 53M
xenoMrna.sql 2020-08-21 19:59 2.1K
xenoMrna.txt.gz 2020-08-21 19:59 188M
xenoRefFlat.sql 2020-08-21 19:59 1.7K
xenoRefFlat.txt.gz 2020-08-21 19:59 21M
xenoRefGene.sql 2020-08-21 19:59 2.0K
xenoRefGene.txt.gz 2020-08-21 19:59 23M
xenoRefSeqAli.sql 2020-08-21 19:59 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 19:59 20M