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 -
nestedRepeats.sql 2011-11-22 15:47 1.9K
nestedRepeats.txt.gz 2011-11-22 15:47 16M
gold.sql 2011-11-22 15:47 1.6K
gold.txt.gz 2011-11-22 15:47 3.2M
chainGorGor3Link.sql 2011-11-22 15:47 1.5K
chainGorGor3Link.txt.gz 2011-11-22 15:47 121M
chainGorGor3.sql 2011-11-22 15:50 1.6K
chainGorGor3.txt.gz 2011-11-22 15:50 15M
chainHg19.sql 2011-11-22 15:50 1.6K
gc5BaseBw.sql 2011-11-22 15:50 1.2K
gc5BaseBw.txt.gz 2011-11-22 15:50 63
chainHg19.txt.gz 2011-11-22 15:50 16M
simpleRepeat.sql 2011-11-22 15:51 1.9K
simpleRepeat.txt.gz 2011-11-22 15:51 22M
chromInfo.sql 2011-11-22 15:52 1.3K
chromInfo.txt.gz 2011-11-22 15:52 90K
netHg19.sql 2011-11-22 15:52 2.0K
netHg19.txt.gz 2011-11-22 15:52 16M
history.sql 2011-11-22 15:53 1.5K
history.txt.gz 2011-11-22 15:53 433
rmsk.sql 2011-11-22 15:53 1.8K
rmsk.txt.gz 2011-11-22 15:53 128M
gap.sql 2011-11-22 15:54 1.5K
gap.txt.gz 2011-11-22 15:54 2.3M
netGorGor3.sql 2011-11-22 15:54 2.0K
netGorGor3.txt.gz 2011-11-22 15:54 20M
chainHg19Link.sql 2011-11-22 15:54 1.5K
chainHg19Link.txt.gz 2011-11-22 15:55 136M
tRNAs.sql 2012-04-16 03:21 1.7K
tRNAs.txt.gz 2012-04-16 03:21 10K
netMm10.sql 2012-10-21 03:38 2.1K
netMm10.txt.gz 2012-10-21 03:39 70M
chainMm10Link.sql 2012-10-21 03:39 1.5K
chainMm10Link.txt.gz 2012-10-21 03:39 464M
chainMm10.sql 2012-10-21 03:41 1.7K
chainMm10.txt.gz 2012-10-21 03:41 57M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
augustusGene.sql 2015-07-26 16:56 1.9K
augustusGene.txt.gz 2015-07-26 16:56 2.1M
microsat.sql 2015-08-23 22:14 1.5K
microsat.txt.gz 2015-08-23 22:14 320K
xenoMrna.sql 2016-02-21 20:37 2.1K
xenoMrna.txt.gz 2016-02-21 20:37 301M
chromAlias.sql 2016-09-15 18:00 1.4K
chromAlias.txt.gz 2016-09-15 18:00 91K
ensPep.sql 2018-02-04 08:24 1.3K
ensPep.txt.gz 2018-02-04 08:24 6.0M
ensemblSource.sql 2018-02-04 08:24 1.4K
ensemblSource.txt.gz 2018-02-04 08:24 85K
ensGtp.sql 2018-02-04 08:25 1.4K
ensGtp.txt.gz 2018-02-04 08:25 280K
ensGene.sql 2018-02-04 08:25 1.9K
ensemblToGeneName.sql 2018-02-04 08:25 1.4K
ensemblToGeneName.txt.gz 2018-02-04 08:25 154K
ensGene.txt.gz 2018-02-04 08:25 2.2M
all_mrna.sql 2020-08-22 12:49 2.1K
all_mrna.txt.gz 2020-08-22 12:49 8.4K
mrnaOrientInfo.sql 2020-08-22 12:49 1.8K
mrnaOrientInfo.txt.gz 2020-08-22 12:49 3.2K
xenoRefGene.sql 2020-08-22 13:34 2.0K
xenoRefGene.txt.gz 2020-08-22 13:34 33M
xenoRefFlat.sql 2020-08-22 13:34 1.7K
xenoRefFlat.txt.gz 2020-08-22 13:34 30M
xenoRefSeqAli.sql 2020-08-22 13:34 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 13:34 32M
gbLoaded.sql 2020-08-22 13:34 1.6K
gbLoaded.txt.gz 2020-08-22 13:34 15K
trackDb_pushedout.sql 2021-12-27 12:20 2.1K
trackDb_pushedout.txt.gz 2021-12-27 12:20 18K
hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K
hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 677
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 13:51 716
tableDescriptions.sql 2024-04-20 02:03 1.5K
tableDescriptions.txt.gz 2024-04-20 02:03 5.2K
tableList.sql 2024-04-21 03:36 1.6K
tableList.txt.gz 2024-04-21 03:36 2.5K
bigFiles.sql 2024-04-21 03:36 1.4K
bigFiles.txt.gz 2024-04-21 03:36 68