This directory contains a dump of the UCSC genome annotation database for
the Jun. 2011 (GGSC Nleu1.1/nomLeu2) assembly of the gibbon genome (nomLeu2, Gibbon Genome Sequencing Consortium Nleu1.1 (NCBI project 13975, GCA_000146795.2, WGS ADFV01)).
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/313108
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=nomLeu2
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/nomLeu2/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/nomLeu2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu2/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 nomLeu2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu2 --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.
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Name Last modified Size Description
Parent Directory -
nestedRepeats.sql 2012-11-16 11:55 1.9K
nestedRepeats.txt.gz 2012-11-16 11:55 17M
cpgIslandExt.sql 2012-11-16 11:56 1.7K
cpgIslandExt.txt.gz 2012-11-16 11:56 581K
gc5BaseBw.sql 2012-11-16 11:56 1.3K
gc5BaseBw.txt.gz 2012-11-16 11:56 63
simpleRepeat.sql 2012-11-16 11:58 1.9K
simpleRepeat.txt.gz 2012-11-16 11:58 22M
netMm10.sql 2012-11-16 11:58 2.1K
netMm10.txt.gz 2012-11-16 11:58 70M
chainMm10.sql 2012-11-16 11:58 1.7K
history.sql 2012-11-16 11:58 1.6K
history.txt.gz 2012-11-16 11:58 513
chainMm10.txt.gz 2012-11-16 11:58 57M
genscan.sql 2012-11-16 11:58 1.7K
genscan.txt.gz 2012-11-16 11:58 2.7M
gold.sql 2012-11-16 11:58 1.7K
gold.txt.gz 2012-11-16 11:58 3.2M
rmsk.sql 2012-11-16 11:58 1.9K
rmsk.txt.gz 2012-11-16 11:59 130M
chainMm10Link.sql 2012-11-16 11:59 1.5K
chainMm10Link.txt.gz 2012-11-16 12:00 463M
windowmaskerSdust.sql 2012-11-16 12:02 1.5K
windowmaskerSdust.txt.gz 2012-11-16 12:03 139M
gap.sql 2012-11-16 12:03 1.6K
gap.txt.gz 2012-11-16 12:03 2.3M
chromInfo.sql 2012-11-16 12:03 1.4K
chromInfo.txt.gz 2012-11-16 12:03 90K
cytoBandIdeo.sql 2013-04-28 19:26 1.5K
cytoBandIdeo.txt.gz 2013-04-28 19:26 88K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:23 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:23 1.3M
augustusGene.sql 2015-07-26 16:56 1.9K
augustusGene.txt.gz 2015-07-26 16:56 2.1M
microsat.sql 2015-08-23 22:22 1.5K
microsat.txt.gz 2015-08-23 22:22 320K
xenoMrna.sql 2016-02-21 20:41 2.1K
xenoMrna.txt.gz 2016-02-21 20:42 314M
xenoRefGene.sql 2020-08-22 12:49 2.0K
xenoRefGene.txt.gz 2020-08-22 12:49 42M
xenoRefFlat.sql 2020-08-22 12:49 1.7K
xenoRefFlat.txt.gz 2020-08-22 12:49 38M
xenoRefSeqAli.sql 2020-08-22 12:49 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 12:49 44M
gbLoaded.sql 2020-08-22 12:49 1.6K
gbLoaded.txt.gz 2020-08-22 12:49 23K
trackDb.sql 2023-03-28 13:51 2.1K
trackDb.txt.gz 2023-03-28 13:51 18K
hgFindSpec.sql 2023-03-28 13:51 1.8K
hgFindSpec.txt.gz 2023-03-28 13:51 491
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 4.7K
tableList.sql 2024-11-17 03:37 1.6K
tableList.txt.gz 2024-11-17 03:37 1.9K
bigFiles.sql 2024-11-17 03:37 1.4K
bigFiles.txt.gz 2024-11-17 03:37 68