This directory contains a dump of the UCSC genome annotation database for the
Oct. 2012 (Nleu_3.0/nomLeu3) assembly of the gibbon genome
(nomLeu3, Gibbon 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/480
http://www.ncbi.nlm.nih.gov/genome/assembly/506498
http://www.ncbi.nlm.nih.gov/bioproject/13975
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=nomLeu3
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/nomLeu3/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/nomLeu3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/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 nomLeu3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 -
netHg19.sql 2013-05-23 11:45 2.1K
netHg19.txt.gz 2013-05-23 11:45 16M
nestedRepeats.sql 2013-05-23 11:45 1.9K
nestedRepeats.txt.gz 2013-05-23 11:45 16M
chromInfo.sql 2013-05-23 11:45 1.4K
chromInfo.txt.gz 2013-05-23 11:45 92K
rmsk.sql 2013-05-23 11:46 1.9K
rmsk.txt.gz 2013-05-23 11:47 129M
genscan.sql 2013-05-23 11:47 1.7K
genscan.txt.gz 2013-05-23 11:47 2.7M
history.sql 2013-05-23 11:47 1.6K
history.txt.gz 2013-05-23 11:47 390
genscanSubopt.sql 2013-05-23 11:48 1.6K
genscanSubopt.txt.gz 2013-05-23 11:48 5.6M
cpgIslandExt.sql 2013-05-23 11:50 1.7K
cpgIslandExt.txt.gz 2013-05-23 11:50 594K
simpleRepeat.sql 2013-05-23 11:50 1.9K
simpleRepeat.txt.gz 2013-05-23 11:50 23M
gap.sql 2013-05-23 11:50 1.6K
chainHg19Link.sql 2013-05-23 11:50 1.5K
gap.txt.gz 2013-05-23 11:50 2.4M
chainHg19Link.txt.gz 2013-05-23 11:50 138M
gc5BaseBw.sql 2013-05-23 11:51 1.3K
gc5BaseBw.txt.gz 2013-05-23 11:51 63
chainHg19.sql 2013-05-23 11:52 1.7K
chainHg19.txt.gz 2013-05-23 11:52 16M
windowmaskerSdust.sql 2013-05-23 11:52 1.5K
windowmaskerSdust.txt.gz 2013-05-23 11:52 140M
gold.sql 2013-05-23 11:53 1.7K
gold.txt.gz 2013-05-23 11:53 3.3M
ucscToINSDC.sql 2013-09-15 17:09 1.4K
ucscToINSDC.txt.gz 2013-09-15 17:09 139K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:28 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:28 1.3M
chainTarSyr2Link.sql 2015-05-25 06:26 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 06:27 1.1G
netTarSyr2.sql 2015-05-25 06:31 2.1K
netTarSyr2.txt.gz 2015-05-25 06:31 66M
chainTarSyr2.sql 2015-05-25 06:32 1.7K
chainTarSyr2.txt.gz 2015-05-25 06:32 278M
augustusGene.sql 2015-07-26 17:03 1.9K
augustusGene.txt.gz 2015-07-26 17:03 2.1M
microsat.sql 2015-08-23 22:29 1.5K
microsat.txt.gz 2015-08-23 22:29 329K
geneid.sql 2015-11-22 19:41 1.9K
geneid.txt.gz 2015-11-22 19:41 2.1M
chainHg38.sql 2018-01-07 09:29 1.7K
chainHg38.txt.gz 2018-01-07 09:29 246M
chainHg38Link.sql 2018-01-07 09:30 1.5K
chainHg38Link.txt.gz 2018-01-07 09:31 753M
netHg38.sql 2018-01-07 09:34 2.1K
netHg38.txt.gz 2018-01-07 09:34 16M
chromAlias.sql 2018-02-04 08:28 1.4K
chromAlias.txt.gz 2018-02-04 08:28 202K
ucscToRefSeq.sql 2018-02-04 08:28 1.4K
ucscToRefSeq.txt.gz 2018-02-04 08:28 142K
xenoMrna.sql 2020-08-19 21:23 2.1K
xenoMrna.txt.gz 2020-08-19 21:23 245M
xenoRefGene.sql 2020-08-19 21:38 2.0K
xenoRefGene.txt.gz 2020-08-19 21:38 26M
xenoRefFlat.sql 2020-08-19 21:38 1.7K
xenoRefFlat.txt.gz 2020-08-19 21:38 23M
xenoRefSeqAli.sql 2020-08-19 21:42 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 21:42 26M
gbLoaded.sql 2020-08-19 21:42 1.6K
gbLoaded.txt.gz 2020-08-19 21:42 29K
ensGene.sql 2021-05-25 14:40 1.9K
ensGene.txt.gz 2021-05-25 14:40 2.9M
ensGtp.sql 2021-05-25 14:40 1.4K
ensGtp.txt.gz 2021-05-25 14:40 476K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:40 222K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 138K
ensPep.sql 2021-05-25 14:41 1.3K
ensPep.txt.gz 2021-05-25 14:41 12M
ncbiRefSeq.sql 2022-05-26 12:18 2.0K
ncbiRefSeq.txt.gz 2022-05-26 12:18 2.8M
ncbiRefSeqCurated.sql 2022-05-26 12:18 2.0K
ncbiRefSeqCurated.txt.gz 2022-05-26 12:18 2.5K
ncbiRefSeqPredicted.sql 2022-05-26 12:18 2.0K
ncbiRefSeqPredicted.txt.gz 2022-05-26 12:18 2.8M
ncbiRefSeqLink.sql 2022-05-26 12:19 2.0K
ncbiRefSeqLink.txt.gz 2022-05-26 12:19 1.3M
ncbiRefSeqPsl.sql 2022-05-26 12:19 2.1K
ncbiRefSeqPsl.txt.gz 2022-05-26 12:19 3.3M
ncbiRefSeqPepTable.sql 2022-05-26 12:22 1.4K
ncbiRefSeqPepTable.txt.gz 2022-05-26 12:22 8.2M
ncbiRefSeqOther.sql 2022-05-26 12:22 1.3K
ncbiRefSeqOther.txt.gz 2022-05-26 12:22 75
extNcbiRefSeq.sql 2022-05-26 12:22 1.5K
extNcbiRefSeq.txt.gz 2022-05-26 12:22 91
ncbiRefSeqCds.sql 2022-05-26 12:22 1.4K
ncbiRefSeqCds.txt.gz 2022-05-26 12:22 264K
seqNcbiRefSeq.sql 2022-05-26 12:22 1.6K
seqNcbiRefSeq.txt.gz 2022-05-26 12:22 668K
cytoBandIdeo.sql 2022-05-26 12:48 1.5K
cytoBandIdeo.txt.gz 2022-05-26 12:48 93K
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 31K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 31K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.2K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.2K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.2K
tableList.sql 2024-04-14 03:35 1.6K
tableList.txt.gz 2024-04-14 03:35 3.2K
bigFiles.sql 2024-04-14 03:35 1.4K
bigFiles.txt.gz 2024-04-14 03:35 94