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.
---------------------------------------------------------------
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 -
xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M
xenoRefSeqAli.sql 2020-08-19 14:06 2.1K
xenoRefGene.txt.gz 2020-08-19 14:06 36M
xenoRefGene.sql 2020-08-19 14:06 2.0K
xenoRefFlat.txt.gz 2020-08-19 14:06 33M
xenoRefFlat.sql 2020-08-19 14:06 1.7K
xenoMrna.txt.gz 2020-08-19 13:31 302M
xenoMrna.sql 2020-08-19 13:31 2.1K
ucscToINSDC.txt.gz 2013-09-15 15:48 19K
ucscToINSDC.sql 2013-09-15 15:48 1.4K
trackDb_pushedout.txt.gz 2023-12-05 13:52 30K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 30K
trackDb.sql 2023-12-05 13:52 2.1K
tableList.txt.gz 2024-04-21 03:07 3.9K
tableList.sql 2024-04-21 03:07 1.6K
tableDescriptions.txt.gz 2024-04-20 02:03 6.9K
tableDescriptions.sql 2024-04-20 02:03 1.5K
tRNAs.txt.gz 2012-04-23 04:53 56K
tRNAs.sql 2012-04-23 04:53 1.7K
simpleRepeat.txt.gz 2010-03-24 14:12 11M
simpleRepeat.sql 2010-03-24 14:12 2.0K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
rmsk.txt.gz 2010-03-24 14:20 148M
rmsk.sql 2010-03-24 14:20 2.0K
refSeqAli.txt.gz 2016-09-18 10:07 2.3K
refSeqAli.sql 2016-09-18 10:07 2.1K
refGene.txt.gz 2020-08-19 14:02 2.2K
refGene.sql 2020-08-19 14:02 1.9K
refFlat.txt.gz 2020-08-19 14:02 2.1K
refFlat.sql 2020-08-19 14:02 1.7K
quality.txt.gz 2010-03-24 14:13 55M
quality.sql 2010-03-24 14:12 1.9K
netNeoSch1.txt.gz 2020-07-15 21:44 77M
netNeoSch1.sql 2020-07-15 21:44 2.1K
netMonDom5.txt.gz 2011-11-21 18:27 19M
netMonDom5.sql 2011-11-21 18:27 2.0K
netMm39.txt.gz 2020-11-25 04:23 58M
netMm39.sql 2020-11-25 04:23 2.1K
netMm10.txt.gz 2013-10-27 17:05 58M
netMm10.sql 2013-10-27 17:05 2.1K
netHg19.txt.gz 2010-03-24 14:22 74M
netHg19.sql 2010-03-24 14:22 2.3K
nestedRepeats.txt.gz 2010-03-24 14:22 17M
nestedRepeats.sql 2010-03-24 14:22 2.0K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
mrnaOrientInfo.txt.gz 2019-07-14 07:57 958
mrnaOrientInfo.sql 2019-07-14 07:57 1.8K
microsat.txt.gz 2015-08-23 20:42 138K
microsat.sql 2015-08-23 20:42 1.5K
history.txt.gz 2010-03-24 14:22 573
history.sql 2010-03-24 14:22 1.6K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.4K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.4K
hgFindSpec.sql 2023-12-05 13:52 1.8K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.4K
gold.txt.gz 2010-03-24 14:13 1.7M
gold.sql 2010-03-24 14:13 1.7K
genscan.txt.gz 2013-12-10 01:52 3.3M
genscan.sql 2013-12-10 01:52 1.7K
geneid.txt.gz 2015-11-22 18:55 2.6M
geneid.sql 2015-11-22 18:55 1.9K
gc5Base.txt.gz 2010-03-24 14:22 13M
gc5Base.sql 2010-03-24 14:22 1.9K
gbLoaded.txt.gz 2020-08-19 14:06 15K
gbLoaded.sql 2020-08-19 14:06 1.6K
gap.txt.gz 2010-03-24 14:03 1.3M
gap.sql 2010-03-24 14:03 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:35 153K
ensemblToGeneName.sql 2021-05-25 14:35 1.4K
ensemblSource.txt.gz 2021-05-25 14:37 86K
ensemblSource.sql 2021-05-25 14:37 1.4K
ensPep.txt.gz 2021-05-25 14:37 7.9M
ensPep.sql 2021-05-25 14:37 1.3K
ensGtp.txt.gz 2021-05-25 14:35 302K
ensGtp.sql 2021-05-25 14:35 1.4K
ensGene.txt.gz 2021-05-25 14:35 2.3M
ensGene.sql 2021-05-25 14:35 1.9K
cytoBandIdeo.txt.gz 2013-04-28 18:08 13K
cytoBandIdeo.sql 2013-04-28 18:08 1.5K
chromInfo.txt.gz 2010-03-24 14:22 13K
chromInfo.sql 2010-03-24 14:22 1.3K
chromAlias.txt.gz 2018-08-05 08:02 23K
chromAlias.sql 2018-08-05 08:02 1.4K
chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M
chainNeoSch1Link.sql 2020-07-15 21:41 1.6K
chainNeoSch1.txt.gz 2020-07-15 21:35 198M
chainNeoSch1.sql 2020-07-15 21:35 1.7K
chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G
chainMonDom5Link.sql 2011-11-21 18:11 1.5K
chainMonDom5.txt.gz 2011-11-21 18:25 398M
chainMonDom5.sql 2011-11-21 18:23 1.6K
chainMm39Link.txt.gz 2020-11-25 04:21 656M
chainMm39Link.sql 2020-11-25 04:21 1.6K
chainMm39.txt.gz 2020-11-25 04:15 90M
chainMm39.sql 2020-11-25 04:15 1.7K
chainMm10Link.txt.gz 2017-04-17 01:54 568M
chainMm10Link.sql 2017-04-17 01:46 1.5K
chainMm10.txt.gz 2013-10-27 17:02 112M
chainMm10.sql 2013-10-27 17:02 1.7K
chainHg19Link.txt.gz 2010-03-24 14:06 959M
chainHg19Link.sql 2010-03-24 14:04 1.5K
chainHg19.txt.gz 2010-03-24 14:02 220M
chainHg19.sql 2010-03-24 14:01 1.8K
blastHg18KG.txt.gz 2010-03-24 14:21 3.9M
blastHg18KG.sql 2010-03-24 14:21 2.3K
bigFiles.txt.gz 2024-04-21 03:07 73
bigFiles.sql 2024-04-21 03:07 1.4K
augustusGene.txt.gz 2015-07-26 16:05 2.3M
augustusGene.sql 2015-07-26 16:05 1.9K
all_mrna.txt.gz 2019-07-14 07:57 2.1K
all_mrna.sql 2019-07-14 07:57 2.1K