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.
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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 -
chainTarSyr2Link.txt.gz 2015-05-25 06:27 1.1G
chainHg38Link.txt.gz 2018-01-07 09:31 753M
chainTarSyr2.txt.gz 2015-05-25 06:32 278M
chainHg38.txt.gz 2018-01-07 09:29 246M
xenoMrna.txt.gz 2020-08-19 21:23 245M
windowmaskerSdust.txt.gz 2013-05-23 11:52 140M
chainHg19Link.txt.gz 2013-05-23 11:50 138M
rmsk.txt.gz 2013-05-23 11:47 129M
netTarSyr2.txt.gz 2015-05-25 06:31 66M
xenoRefSeqAli.txt.gz 2020-08-19 21:42 26M
xenoRefGene.txt.gz 2020-08-19 21:38 26M
xenoRefFlat.txt.gz 2020-08-19 21:38 23M
simpleRepeat.txt.gz 2013-05-23 11:50 23M
netHg38.txt.gz 2018-01-07 09:34 16M
nestedRepeats.txt.gz 2013-05-23 11:45 16M
chainHg19.txt.gz 2013-05-23 11:52 16M
netHg19.txt.gz 2013-05-23 11:45 16M
ensPep.txt.gz 2021-05-25 14:41 12M
ncbiRefSeqPepTable.txt.gz 2022-05-26 12:22 8.2M
genscanSubopt.txt.gz 2013-05-23 11:48 5.6M
gold.txt.gz 2013-05-23 11:53 3.3M
ncbiRefSeqPsl.txt.gz 2022-05-26 12:19 3.3M
ensGene.txt.gz 2021-05-25 14:40 2.9M
ncbiRefSeq.txt.gz 2022-05-26 12:18 2.8M
ncbiRefSeqPredicted.txt.gz 2022-05-26 12:18 2.8M
genscan.txt.gz 2013-05-23 11:47 2.7M
gap.txt.gz 2013-05-23 11:50 2.4M
geneid.txt.gz 2015-11-22 19:41 2.1M
augustusGene.txt.gz 2015-07-26 17:03 2.1M
ncbiRefSeqLink.txt.gz 2022-05-26 12:19 1.3M
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:28 1.3M
seqNcbiRefSeq.txt.gz 2022-05-26 12:22 668K
cpgIslandExt.txt.gz 2013-05-23 11:50 594K
ensGtp.txt.gz 2021-05-25 14:40 476K
microsat.txt.gz 2015-08-23 22:29 329K
ncbiRefSeqCds.txt.gz 2022-05-26 12:22 264K
ensemblToGeneName.txt.gz 2021-05-25 14:40 222K
chromAlias.txt.gz 2018-02-04 08:28 202K
ucscToRefSeq.txt.gz 2018-02-04 08:28 142K
ucscToINSDC.txt.gz 2013-09-15 17:09 139K
ensemblSource.txt.gz 2021-05-25 14:41 138K
cytoBandIdeo.txt.gz 2022-05-26 12:48 93K
chromInfo.txt.gz 2013-05-23 11:45 92K
trackDb.txt.gz 2023-12-05 13:50 31K
gbLoaded.txt.gz 2020-08-19 21:42 29K
tableDescriptions.txt.gz 2024-12-28 02:10 6.2K
tableList.txt.gz 2024-12-29 03:31 3.1K
ncbiRefSeqCurated.txt.gz 2022-05-26 12:18 2.5K
xenoRefSeqAli.sql 2020-08-19 21:42 2.1K
ncbiRefSeqPsl.sql 2022-05-26 12:19 2.1K
xenoMrna.sql 2020-08-19 21:23 2.1K
netTarSyr2.sql 2015-05-25 06:31 2.1K
netHg19.sql 2013-05-23 11:45 2.1K
netHg38.sql 2018-01-07 09:34 2.1K
trackDb.sql 2023-12-05 13:50 2.1K
ncbiRefSeqLink.sql 2022-05-26 12:19 2.0K
ncbiRefSeqPredicted.sql 2022-05-26 12:18 2.0K
ncbiRefSeqCurated.sql 2022-05-26 12:18 2.0K
xenoRefGene.sql 2020-08-19 21:38 2.0K
ncbiRefSeq.sql 2022-05-26 12:18 2.0K
ensGene.sql 2021-05-25 14:40 1.9K
augustusGene.sql 2015-07-26 17:03 1.9K
nestedRepeats.sql 2013-05-23 11:45 1.9K
simpleRepeat.sql 2013-05-23 11:50 1.9K
geneid.sql 2015-11-22 19:41 1.9K
rmsk.sql 2013-05-23 11:46 1.9K
hgFindSpec.sql 2023-12-05 13:50 1.8K
xenoRefFlat.sql 2020-08-19 21:38 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 17:28 1.7K
chainTarSyr2.sql 2015-05-25 06:32 1.7K
chainHg19.sql 2013-05-23 11:52 1.7K
chainHg38.sql 2018-01-07 09:29 1.7K
cpgIslandExt.sql 2013-05-23 11:50 1.7K
genscan.sql 2013-05-23 11:47 1.7K
gold.sql 2013-05-23 11:53 1.7K
gbLoaded.sql 2020-08-19 21:42 1.6K
gap.sql 2013-05-23 11:50 1.6K
tableList.sql 2024-12-29 03:31 1.6K
history.sql 2013-05-23 11:47 1.6K
seqNcbiRefSeq.sql 2022-05-26 12:22 1.6K
genscanSubopt.sql 2013-05-23 11:48 1.6K
chainTarSyr2Link.sql 2015-05-25 06:26 1.5K
cytoBandIdeo.sql 2022-05-26 12:48 1.5K
chainHg19Link.sql 2013-05-23 11:50 1.5K
chainHg38Link.sql 2018-01-07 09:30 1.5K
windowmaskerSdust.sql 2013-05-23 11:52 1.5K
microsat.sql 2015-08-23 22:29 1.5K
extNcbiRefSeq.sql 2022-05-26 12:22 1.5K
tableDescriptions.sql 2024-12-28 02:10 1.5K
ensGtp.sql 2021-05-25 14:40 1.4K
ucscToRefSeq.sql 2018-02-04 08:28 1.4K
ucscToINSDC.sql 2013-09-15 17:09 1.4K
chromAlias.sql 2018-02-04 08:28 1.4K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
bigFiles.sql 2024-12-29 03:31 1.4K
chromInfo.sql 2013-05-23 11:45 1.4K
ncbiRefSeqPepTable.sql 2022-05-26 12:22 1.4K
ensemblSource.sql 2021-05-25 14:41 1.4K
ncbiRefSeqCds.sql 2022-05-26 12:22 1.4K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2021-05-25 14:41 1.3K
ncbiRefSeqOther.sql 2022-05-26 12:22 1.3K
gc5BaseBw.sql 2013-05-23 11:51 1.3K
hgFindSpec.txt.gz 2023-12-05 13:50 1.2K
history.txt.gz 2013-05-23 11:47 390
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-12-29 03:31 94
extNcbiRefSeq.txt.gz 2022-05-26 12:22 91
ncbiRefSeqOther.txt.gz 2022-05-26 12:22 75
gc5BaseBw.txt.gz 2013-05-23 11:51 63