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.
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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 -
gc5BaseBw.txt.gz 2016-09-18 08:19 66
ncbiRefSeqOther.txt.gz 2018-02-09 14:16 75
grcIncidentDb.txt.gz 2018-05-13 05:42 77
extNcbiRefSeq.txt.gz 2018-02-09 14:16 91
bigFiles.txt.gz 2024-04-28 03:07 120
grp.txt.gz 2016-09-18 08:19 213
history.txt.gz 2016-09-18 08:19 816
snp147ExceptionDesc.txt.gz 2017-04-02 19:06 1.0K
gc5BaseBw.sql 2016-09-18 08:19 1.3K
grcIncidentDb.sql 2018-05-13 05:42 1.3K
ncbiRefSeqOther.sql 2018-02-09 14:16 1.3K
ensPep.sql 2018-08-05 06:42 1.3K
snp147Seq.sql 2017-04-02 19:06 1.3K
grp.sql 2016-09-18 08:19 1.3K
ensemblSource.sql 2018-08-05 06:42 1.4K
ncbiRefSeqCds.sql 2018-02-09 14:16 1.4K
ncbiRefSeqPepTable.sql 2018-02-09 14:16 1.4K
chromInfo.sql 2016-09-18 08:19 1.4K
hgFindSpec.txt.gz 2023-12-05 13:51 1.4K
snp147ExceptionDesc.sql 2017-04-02 19:06 1.4K
ensemblToGeneName.sql 2018-08-05 06:43 1.4K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.4K
bigFiles.sql 2024-04-28 03:07 1.4K
ensGtp.sql 2018-08-05 06:42 1.4K
chromAlias.sql 2017-09-03 05:25 1.4K
ucscToINSDC.sql 2016-09-18 08:20 1.4K
ucscToRefSeq.sql 2016-09-18 08:20 1.4K
tableDescriptions.sql 2024-04-27 02:03 1.5K
extNcbiRefSeq.sql 2018-02-09 14:16 1.5K
microsat.sql 2016-09-18 08:19 1.5K
windowmaskerSdust.sql 2016-09-18 08:20 1.5K
cytoBandIdeo.sql 2016-09-18 08:19 1.5K
chainRn6Link.sql 2016-09-18 08:19 1.5K
chainHg38Link.sql 2016-09-18 08:17 1.5K
chainMm10Link.sql 2016-09-18 08:18 1.5K
chainAquChr2Link.sql 2018-04-01 06:28 1.5K
chainMelGal5Link.sql 2017-03-19 21:20 1.5K
chainXenTro9Link.sql 2017-12-14 10:29 1.5K
chainDanRer10Link.sql 2016-09-18 08:17 1.6K
seqNcbiRefSeq.sql 2018-02-09 14:16 1.6K
history.sql 2016-09-18 08:19 1.6K
tableList.sql 2024-04-28 03:07 1.6K
gap.sql 2016-09-18 08:19 1.6K
gbLoaded.sql 2020-08-21 19:59 1.6K
gold.sql 2016-09-18 08:19 1.7K
genscan.sql 2016-09-18 08:19 1.7K
cpgIslandExt.sql 2016-09-18 08:19 1.7K
chainRn6.sql 2016-09-18 08:19 1.7K
chainHg38.sql 2016-09-18 08:17 1.7K
chainMm10.sql 2016-09-18 08:18 1.7K
chainAquChr2.sql 2018-04-01 06:28 1.7K
chainMelGal5.sql 2017-03-19 21:14 1.7K
chainXenTro9.sql 2017-12-14 10:29 1.7K
cpgIslandExtUnmasked.sql 2016-09-18 08:19 1.7K
chainDanRer10.sql 2016-09-18 08:17 1.7K
refFlat.sql 2020-08-21 19:59 1.7K
snp147CodingDbSnp.sql 2017-04-02 19:05 1.7K
xenoRefFlat.sql 2020-08-21 19:59 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
estOrientInfo.sql 2020-05-08 00:49 1.8K
mrnaOrientInfo.sql 2020-08-21 19:59 1.8K
rmsk.sql 2016-09-18 08:20 1.9K
ensGene.sql 2018-08-05 06:42 1.9K
simpleRepeat.sql 2016-09-18 08:20 1.9K
nestedRepeats.sql 2016-09-18 08:19 1.9K
augustusGene.sql 2016-09-18 08:17 1.9K
refGene.sql 2020-08-21 19:59 1.9K
ncbiRefSeq.sql 2018-02-09 13:42 2.0K
xenoRefGene.sql 2020-08-21 19:59 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:42 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:42 2.0K
ncbiRefSeqLink.sql 2018-02-09 13:42 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
netRn6.sql 2016-09-18 08:20 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
netHg38.sql 2016-09-18 08:19 2.1K
netMm10.sql 2016-09-18 08:19 2.1K
netAquChr2.sql 2018-04-01 06:31 2.1K
netMelGal5.sql 2017-03-19 22:25 2.1K
netXenTro9.sql 2017-12-14 10:29 2.1K
netDanRer10.sql 2016-09-18 08:19 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 19:59 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:42 2.1K
xenoRefSeqAli.sql 2020-08-21 19:59 2.1K
snp147.sql 2017-04-02 18:42 3.0K
snp147Mult.sql 2017-04-02 19:06 3.0K
tableList.txt.gz 2024-04-28 03:07 5.1K
tableDescriptions.txt.gz 2024-04-27 02:03 7.9K
gap.txt.gz 2016-09-18 08:19 18K
microsat.txt.gz 2016-09-18 08:19 25K
gbLoaded.txt.gz 2020-08-21 19:59 44K
trackDb.txt.gz 2023-12-05 13:51 53K
trackDb_pushedout.txt.gz 2023-12-05 13:51 53K
cytoBandIdeo.txt.gz 2016-09-18 08:19 116K
ensemblSource.txt.gz 2018-08-05 06:42 121K
chromInfo.txt.gz 2016-09-18 08:19 127K
ensemblToGeneName.txt.gz 2018-08-05 06:43 167K
ucscToRefSeq.txt.gz 2016-09-18 08:20 180K
ucscToINSDC.txt.gz 2016-09-18 08:20 181K
chromAlias.txt.gz 2017-09-03 05:25 261K
gold.txt.gz 2016-09-18 08:19 286K
ncbiRefSeqCds.txt.gz 2018-02-09 14:16 317K
ensGtp.txt.gz 2018-08-05 06:42 387K
cpgIslandExt.txt.gz 2016-09-18 08:19 536K
mrnaOrientInfo.txt.gz 2020-08-21 19:59 590K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:42 657K
refFlat.txt.gz 2020-08-21 19:59 676K
refGene.txt.gz 2020-08-21 19:59 726K
cpgIslandExtUnmasked.txt.gz 2016-09-18 08:19 746K
refSeqAli.txt.gz 2020-08-21 19:59 755K
seqNcbiRefSeq.txt.gz 2018-02-09 14:16 871K
snp147Mult.txt.gz 2017-04-02 19:06 1.2M
nestedRepeats.txt.gz 2016-09-18 08:19 1.5M
ncbiRefSeqLink.txt.gz 2018-02-09 13:42 1.6M
genscan.txt.gz 2016-09-18 08:19 1.7M
augustusGene.txt.gz 2016-09-18 08:17 1.7M
all_mrna.txt.gz 2020-08-21 19:59 2.0M
ensGene.txt.gz 2018-08-05 06:42 2.4M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:42 2.6M
ncbiRefSeq.txt.gz 2018-02-09 13:42 3.0M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:42 4.3M
netXenTro9.txt.gz 2017-12-14 10:29 5.5M
netDanRer10.txt.gz 2016-09-18 08:19 5.6M
chainXenTro9.txt.gz 2017-12-14 10:29 6.8M
estOrientInfo.txt.gz 2020-05-08 00:49 8.0M
ensPep.txt.gz 2018-08-05 06:42 8.7M
chainMm10.txt.gz 2016-09-18 08:18 8.9M
netMm10.txt.gz 2016-09-18 08:20 8.9M
netRn6.txt.gz 2016-09-18 08:20 9.1M
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:16 9.2M
netHg38.txt.gz 2016-09-18 08:19 11M
snp147CodingDbSnp.txt.gz 2017-04-02 19:05 12M
chainDanRer10.txt.gz 2016-09-18 08:17 12M
chainRn6.txt.gz 2016-09-18 08:19 14M
simpleRepeat.txt.gz 2016-09-18 08:20 17M
xenoRefSeqAli.txt.gz 2020-08-21 19:59 20M
intronEst.txt.gz 2020-05-08 00:49 21M
xenoRefFlat.txt.gz 2020-08-21 19:59 21M
netMelGal5.txt.gz 2017-03-19 22:25 21M
rmsk.txt.gz 2016-09-18 08:20 22M
xenoRefGene.txt.gz 2020-08-21 19:59 23M
chainXenTro9Link.txt.gz 2017-12-14 10:29 25M
netAquChr2.txt.gz 2018-04-01 06:31 27M
chainHg38.txt.gz 2016-09-18 08:17 27M
all_est.txt.gz 2020-05-08 00:49 39M
windowmaskerSdust.txt.gz 2016-09-18 08:20 53M
chainDanRer10Link.txt.gz 2016-09-18 08:17 54M
chainAquChr2.txt.gz 2018-04-01 06:28 72M
chainMm10Link.txt.gz 2016-09-18 08:18 73M
chainRn6Link.txt.gz 2016-09-18 08:19 96M
snp147Seq.txt.gz 2017-04-02 19:07 128M
chainHg38Link.txt.gz 2016-09-18 08:18 164M
xenoMrna.txt.gz 2020-08-21 19:59 188M
chainMelGal5.txt.gz 2017-03-19 21:16 309M
snp147.txt.gz 2017-04-02 18:52 332M
chainAquChr2Link.txt.gz 2018-04-01 06:29 530M
chainMelGal5Link.txt.gz 2017-03-19 21:27 1.4G