This directory contains a dump of the UCSC genome annotation database for
the Jul. 2009 assembly of the elephant genome
(loxAfr3, Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Broad Institute.
For more information on the elephant genome, see the project website:
http://www.broadinstitute.org/science/projects/mammals-models/elephant/elephant
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=loxAfr3
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/loxAfr3/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/loxAfr3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/loxAfr3/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/
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/
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 loxAfr3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql loxAfr3 --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 -
chainHg19.sql 2010-03-24 14:01 1.8K
chainHg19.txt.gz 2010-03-24 14:02 220M
gap.sql 2010-03-24 14:03 1.6K
gap.txt.gz 2010-03-24 14:03 1.3M
chainHg19Link.sql 2010-03-24 14:04 1.5K
chainHg19Link.txt.gz 2010-03-24 14:06 959M
simpleRepeat.sql 2010-03-24 14:12 2.0K
simpleRepeat.txt.gz 2010-03-24 14:12 11M
quality.sql 2010-03-24 14:12 1.9K
quality.txt.gz 2010-03-24 14:13 55M
gold.sql 2010-03-24 14:13 1.7K
gold.txt.gz 2010-03-24 14:13 1.7M
rmsk.sql 2010-03-24 14:20 2.0K
rmsk.txt.gz 2010-03-24 14:20 148M
blastHg18KG.sql 2010-03-24 14:21 2.3K
blastHg18KG.txt.gz 2010-03-24 14:21 3.9M
history.sql 2010-03-24 14:22 1.6K
history.txt.gz 2010-03-24 14:22 573
chromInfo.sql 2010-03-24 14:22 1.3K
chromInfo.txt.gz 2010-03-24 14:22 13K
nestedRepeats.sql 2010-03-24 14:22 2.0K
nestedRepeats.txt.gz 2010-03-24 14:22 17M
gc5Base.sql 2010-03-24 14:22 1.9K
gc5Base.txt.gz 2010-03-24 14:22 13M
netHg19.sql 2010-03-24 14:22 2.3K
netHg19.txt.gz 2010-03-24 14:22 74M
chainMonDom5Link.sql 2011-11-21 18:11 1.5K
chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G
chainMonDom5.sql 2011-11-21 18:23 1.6K
chainMonDom5.txt.gz 2011-11-21 18:25 398M
netMonDom5.sql 2011-11-21 18:27 2.0K
netMonDom5.txt.gz 2011-11-21 18:27 19M
tRNAs.sql 2012-04-23 04:53 1.7K
tRNAs.txt.gz 2012-04-23 04:53 56K
cytoBandIdeo.sql 2013-04-28 18:08 1.5K
cytoBandIdeo.txt.gz 2013-04-28 18:08 13K
ucscToINSDC.sql 2013-09-15 15:48 1.4K
ucscToINSDC.txt.gz 2013-09-15 15:48 19K
chainMm10.sql 2013-10-27 17:02 1.7K
chainMm10.txt.gz 2013-10-27 17:02 112M
netMm10.sql 2013-10-27 17:05 2.1K
netMm10.txt.gz 2013-10-27 17:05 58M
genscan.sql 2013-12-10 01:52 1.7K
genscan.txt.gz 2013-12-10 01:52 3.3M
grp.sql 2014-03-02 04:14 1.4K
grp.txt.gz 2014-03-02 04:14 208
augustusGene.sql 2015-07-26 16:05 1.9K
augustusGene.txt.gz 2015-07-26 16:05 2.3M
microsat.sql 2015-08-23 20:42 1.5K
microsat.txt.gz 2015-08-23 20:42 138K
geneid.sql 2015-11-22 18:55 1.9K
geneid.txt.gz 2015-11-22 18:55 2.6M
refSeqAli.sql 2016-09-18 10:07 2.1K
refSeqAli.txt.gz 2016-09-18 10:07 2.3K
chainMm10Link.sql 2017-04-17 01:46 1.5K
chainMm10Link.txt.gz 2017-04-17 01:54 568M
chromAlias.sql 2018-08-05 08:02 1.4K
chromAlias.txt.gz 2018-08-05 08:02 23K
mrnaOrientInfo.sql 2019-07-14 07:57 1.8K
mrnaOrientInfo.txt.gz 2019-07-14 07:57 958
all_mrna.sql 2019-07-14 07:57 2.1K
all_mrna.txt.gz 2019-07-14 07:57 2.1K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K
chainNeoSch1.sql 2020-07-15 21:35 1.7K
chainNeoSch1.txt.gz 2020-07-15 21:35 198M
chainNeoSch1Link.sql 2020-07-15 21:41 1.6K
chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M
netNeoSch1.sql 2020-07-15 21:44 2.1K
netNeoSch1.txt.gz 2020-07-15 21:44 77M
xenoMrna.sql 2020-08-19 13:31 2.1K
xenoMrna.txt.gz 2020-08-19 13:31 302M
refGene.sql 2020-08-19 14:02 1.9K
refGene.txt.gz 2020-08-19 14:02 2.2K
refFlat.sql 2020-08-19 14:02 1.7K
refFlat.txt.gz 2020-08-19 14:02 2.1K
xenoRefGene.sql 2020-08-19 14:06 2.0K
xenoRefGene.txt.gz 2020-08-19 14:06 36M
xenoRefFlat.sql 2020-08-19 14:06 1.7K
xenoRefFlat.txt.gz 2020-08-19 14:06 33M
xenoRefSeqAli.sql 2020-08-19 14:06 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M
gbLoaded.sql 2020-08-19 14:06 1.6K
gbLoaded.txt.gz 2020-08-19 14:06 15K
chainMm39.sql 2020-11-25 04:15 1.7K
chainMm39.txt.gz 2020-11-25 04:15 90M
chainMm39Link.sql 2020-11-25 04:21 1.6K
chainMm39Link.txt.gz 2020-11-25 04:21 656M
netMm39.sql 2020-11-25 04:23 2.1K
netMm39.txt.gz 2020-11-25 04:23 58M
ensGene.sql 2021-05-25 14:35 1.9K
ensGene.txt.gz 2021-05-25 14:35 2.3M
ensGtp.sql 2021-05-25 14:35 1.4K
ensGtp.txt.gz 2021-05-25 14:35 302K
ensemblToGeneName.sql 2021-05-25 14:35 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:35 153K
ensemblSource.sql 2021-05-25 14:37 1.4K
ensemblSource.txt.gz 2021-05-25 14:37 86K
ensPep.sql 2021-05-25 14:37 1.3K
ensPep.txt.gz 2021-05-25 14:37 7.9M
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 30K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 6.9K
tableList.sql 2024-11-24 03:06 1.6K
tableList.txt.gz 2024-11-24 03:06 3.8K
bigFiles.sql 2024-11-24 03:06 1.4K
bigFiles.txt.gz 2024-11-24 03:06 73