This directory contains a dump of the UCSC genome annotation database for
the Jan. 2010 (GGSC Nleu1.0/nomLeu1) assembly of the gibbon genome (nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the gibbon genome, see the project website:
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=nomLeu1
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/nomLeu1/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/nomLeu1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/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 nomLeu1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nomLeu1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2011-11-22 15:50 63
bigFiles.txt.gz 2024-04-14 03:34 68
grp.txt.gz 2014-03-02 04:14 208
history.txt.gz 2011-11-22 15:53 433
hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 677
hgFindSpec.txt.gz 2023-03-28 13:51 716
gc5BaseBw.sql 2011-11-22 15:50 1.2K
chromInfo.sql 2011-11-22 15:52 1.3K
ensPep.sql 2018-02-04 08:24 1.3K
grp.sql 2014-03-02 04:14 1.3K
ensemblSource.sql 2018-02-04 08:24 1.4K
ensemblToGeneName.sql 2018-02-04 08:25 1.4K
bigFiles.sql 2024-04-14 03:34 1.4K
ensGtp.sql 2018-02-04 08:25 1.4K
chromAlias.sql 2016-09-15 18:00 1.4K
tableDescriptions.sql 2024-04-13 02:03 1.5K
chainHg19Link.sql 2011-11-22 15:54 1.5K
chainGorGor3Link.sql 2011-11-22 15:47 1.5K
microsat.sql 2015-08-23 22:14 1.5K
history.sql 2011-11-22 15:53 1.5K
gap.sql 2011-11-22 15:54 1.5K
chainMm10Link.sql 2012-10-21 03:39 1.5K
tableList.sql 2024-04-14 03:34 1.6K
gold.sql 2011-11-22 15:47 1.6K
gbLoaded.sql 2020-08-22 13:34 1.6K
chainHg19.sql 2011-11-22 15:50 1.6K
chainGorGor3.sql 2011-11-22 15:50 1.6K
tRNAs.sql 2012-04-16 03:21 1.7K
chainMm10.sql 2012-10-21 03:41 1.7K
xenoRefFlat.sql 2020-08-22 13:34 1.7K
hgFindSpec.sql 2023-03-28 13:51 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K
rmsk.sql 2011-11-22 15:53 1.8K
mrnaOrientInfo.sql 2020-08-22 12:49 1.8K
simpleRepeat.sql 2011-11-22 15:51 1.9K
nestedRepeats.sql 2011-11-22 15:47 1.9K
ensGene.sql 2018-02-04 08:25 1.9K
augustusGene.sql 2015-07-26 16:56 1.9K
xenoRefGene.sql 2020-08-22 13:34 2.0K
netHg19.sql 2011-11-22 15:52 2.0K
netGorGor3.sql 2011-11-22 15:54 2.0K
trackDb.sql 2023-03-28 13:51 2.1K
trackDb_pushedout.sql 2021-12-27 12:20 2.1K
netMm10.sql 2012-10-21 03:38 2.1K
xenoMrna.sql 2016-02-21 20:37 2.1K
all_mrna.sql 2020-08-22 12:49 2.1K
xenoRefSeqAli.sql 2020-08-22 13:34 2.1K
tableList.txt.gz 2024-04-14 03:34 2.5K
mrnaOrientInfo.txt.gz 2020-08-22 12:49 3.2K
tableDescriptions.txt.gz 2024-04-13 02:03 5.2K
all_mrna.txt.gz 2020-08-22 12:49 8.4K
tRNAs.txt.gz 2012-04-16 03:21 10K
gbLoaded.txt.gz 2020-08-22 13:34 15K
trackDb_pushedout.txt.gz 2021-12-27 12:20 18K
trackDb.txt.gz 2023-03-28 13:51 18K
ensemblSource.txt.gz 2018-02-04 08:24 85K
chromInfo.txt.gz 2011-11-22 15:52 90K
chromAlias.txt.gz 2016-09-15 18:00 91K
ensemblToGeneName.txt.gz 2018-02-04 08:25 154K
ensGtp.txt.gz 2018-02-04 08:25 280K
microsat.txt.gz 2015-08-23 22:14 320K
augustusGene.txt.gz 2015-07-26 16:56 2.1M
ensGene.txt.gz 2018-02-04 08:25 2.2M
gap.txt.gz 2011-11-22 15:54 2.3M
gold.txt.gz 2011-11-22 15:47 3.2M
ensPep.txt.gz 2018-02-04 08:24 6.0M
chainGorGor3.txt.gz 2011-11-22 15:50 15M
chainHg19.txt.gz 2011-11-22 15:50 16M
netHg19.txt.gz 2011-11-22 15:52 16M
nestedRepeats.txt.gz 2011-11-22 15:47 16M
netGorGor3.txt.gz 2011-11-22 15:54 20M
simpleRepeat.txt.gz 2011-11-22 15:51 22M
xenoRefFlat.txt.gz 2020-08-22 13:34 30M
xenoRefSeqAli.txt.gz 2020-08-22 13:34 32M
xenoRefGene.txt.gz 2020-08-22 13:34 33M
chainMm10.txt.gz 2012-10-21 03:41 57M
netMm10.txt.gz 2012-10-21 03:39 70M
chainGorGor3Link.txt.gz 2011-11-22 15:47 121M
rmsk.txt.gz 2011-11-22 15:53 128M
chainHg19Link.txt.gz 2011-11-22 15:55 136M
xenoMrna.txt.gz 2016-02-21 20:37 301M
chainMm10Link.txt.gz 2012-10-21 03:39 464M