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 -
chainMonDom5Link.txt.gz 2011-11-21 18:15 1.1G
chainHg19Link.txt.gz 2010-03-24 14:06 959M
chainNeoSch1Link.txt.gz 2020-07-15 21:41 898M
chainMm39Link.txt.gz 2020-11-25 04:21 656M
chainMm10Link.txt.gz 2017-04-17 01:54 568M
chainMonDom5.txt.gz 2011-11-21 18:25 398M
xenoMrna.txt.gz 2020-08-19 13:31 302M
chainHg19.txt.gz 2010-03-24 14:02 220M
chainNeoSch1.txt.gz 2020-07-15 21:35 198M
rmsk.txt.gz 2010-03-24 14:20 148M
chainMm10.txt.gz 2013-10-27 17:02 112M
chainMm39.txt.gz 2020-11-25 04:15 90M
netNeoSch1.txt.gz 2020-07-15 21:44 77M
netHg19.txt.gz 2010-03-24 14:22 74M
netMm10.txt.gz 2013-10-27 17:05 58M
netMm39.txt.gz 2020-11-25 04:23 58M
quality.txt.gz 2010-03-24 14:13 55M
xenoRefGene.txt.gz 2020-08-19 14:06 36M
xenoRefSeqAli.txt.gz 2020-08-19 14:06 35M
xenoRefFlat.txt.gz 2020-08-19 14:06 33M
netMonDom5.txt.gz 2011-11-21 18:27 19M
nestedRepeats.txt.gz 2010-03-24 14:22 17M
gc5Base.txt.gz 2010-03-24 14:22 13M
simpleRepeat.txt.gz 2010-03-24 14:12 11M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M
ensPep.txt.gz 2021-05-25 14:37 7.9M
blastHg18KG.txt.gz 2010-03-24 14:21 3.9M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M
genscan.txt.gz 2013-12-10 01:52 3.3M
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M
geneid.txt.gz 2015-11-22 18:55 2.6M
augustusGene.txt.gz 2015-07-26 16:05 2.3M
ensGene.txt.gz 2021-05-25 14:35 2.3M
gold.txt.gz 2010-03-24 14:13 1.7M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M
gap.txt.gz 2010-03-24 14:03 1.3M
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 702K
ensGtp.txt.gz 2021-05-25 14:35 302K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 285K
ensemblToGeneName.txt.gz 2021-05-25 14:35 153K
microsat.txt.gz 2015-08-23 20:42 138K
ensemblSource.txt.gz 2021-05-25 14:37 86K
tRNAs.txt.gz 2012-04-23 04:53 56K
trackDb.txt.gz 2023-12-05 13:52 30K
chromAlias.txt.gz 2018-08-05 08:02 23K
ucscToINSDC.txt.gz 2013-09-15 15:48 19K
gbLoaded.txt.gz 2020-08-19 14:06 15K
chromInfo.txt.gz 2010-03-24 14:22 13K
cytoBandIdeo.txt.gz 2013-04-28 18:08 13K
tableDescriptions.txt.gz 2024-11-23 02:03 6.9K
tableList.txt.gz 2024-11-24 03:06 3.8K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.5K
netHg19.sql 2010-03-24 14:22 2.3K
refSeqAli.txt.gz 2016-09-18 10:07 2.3K
blastHg18KG.sql 2010-03-24 14:21 2.3K
refGene.txt.gz 2020-08-19 14:02 2.2K
xenoRefSeqAli.sql 2020-08-19 14:06 2.1K
xenoMrna.sql 2020-08-19 13:31 2.1K
netNeoSch1.sql 2020-07-15 21:44 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
netMm39.sql 2020-11-25 04:23 2.1K
refSeqAli.sql 2016-09-18 10:07 2.1K
all_mrna.sql 2019-07-14 07:57 2.1K
netMm10.sql 2013-10-27 17:05 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
refFlat.txt.gz 2020-08-19 14:02 2.1K
all_mrna.txt.gz 2019-07-14 07:57 2.1K
simpleRepeat.sql 2010-03-24 14:12 2.0K
netMonDom5.sql 2011-11-21 18:27 2.0K
nestedRepeats.sql 2010-03-24 14:22 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
rmsk.sql 2010-03-24 14:20 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
xenoRefGene.sql 2020-08-19 14:06 2.0K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
refGene.sql 2020-08-19 14:02 1.9K
ensGene.sql 2021-05-25 14:35 1.9K
augustusGene.sql 2015-07-26 16:05 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
geneid.sql 2015-11-22 18:55 1.9K
quality.sql 2010-03-24 14:12 1.9K
gc5Base.sql 2010-03-24 14:22 1.9K
mrnaOrientInfo.sql 2019-07-14 07:57 1.8K
chainHg19.sql 2010-03-24 14:01 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-08-19 14:06 1.7K
chainNeoSch1.sql 2020-07-15 21:35 1.7K
refFlat.sql 2020-08-19 14:02 1.7K
chainMm39.sql 2020-11-25 04:15 1.7K
gold.sql 2010-03-24 14:13 1.7K
chainMm10.sql 2013-10-27 17:02 1.7K
tRNAs.sql 2012-04-23 04:53 1.7K
genscan.sql 2013-12-10 01:52 1.7K
chainMonDom5.sql 2011-11-21 18:23 1.6K
gap.sql 2010-03-24 14:03 1.6K
gbLoaded.sql 2020-08-19 14:06 1.6K
chainNeoSch1Link.sql 2020-07-15 21:41 1.6K
tableList.sql 2024-11-24 03:06 1.6K
chainMm39Link.sql 2020-11-25 04:21 1.6K
history.sql 2010-03-24 14:22 1.6K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
chainMm10Link.sql 2017-04-17 01:46 1.5K
chainHg19Link.sql 2010-03-24 14:04 1.5K
cytoBandIdeo.sql 2013-04-28 18:08 1.5K
microsat.sql 2015-08-23 20:42 1.5K
chainMonDom5Link.sql 2011-11-21 18:11 1.5K
ensGtp.sql 2021-05-25 14:35 1.4K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ucscToINSDC.sql 2013-09-15 15:48 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
chromAlias.sql 2018-08-05 08:02 1.4K
hgFindSpec.txt.gz 2023-12-05 13:52 1.4K
ensemblToGeneName.sql 2021-05-25 14:35 1.4K
grp.sql 2014-03-02 04:14 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ensemblSource.sql 2021-05-25 14:37 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ensPep.sql 2021-05-25 14:37 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
chromInfo.sql 2010-03-24 14:22 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
mrnaOrientInfo.txt.gz 2019-07-14 07:57 958
history.txt.gz 2010-03-24 14:22 573
grp.txt.gz 2014-03-02 04:14 208
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
bigFiles.txt.gz 2024-11-24 03:06 73