This directory contains a dump of the UCSC genome annotation database for
the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly of the panda genome
(ailMel1, BGI-Shenzhen AilMel 1.0 Dec. 2009),
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the BGI-Shenzhen sequencing center,
Beijing Genomics Institute at Shenzhen.
For more information on the panda genome, see the project website:
http://www.genomics.cn/en/index.php
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=ailMel1
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/ailMel1/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/ailMel1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/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 ailMel1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ailMel1 --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 2010-04-19 17:33 1.6K
history.sql 2010-04-19 17:33 1.5K
history.txt.gz 2010-04-19 17:33 520
chainHg19.txt.gz 2010-04-19 17:33 13M
nestedRepeats.sql 2010-04-19 17:33 1.9K
nestedRepeats.txt.gz 2010-04-19 17:33 11M
netHg19.sql 2010-04-19 17:33 2.0K
netHg19.txt.gz 2010-04-19 17:33 50M
gold.sql 2010-04-19 17:36 1.6K
chainMonDom5.sql 2010-04-19 17:36 1.6K
gold.txt.gz 2010-04-19 17:36 2.4M
chainMonDom5.txt.gz 2010-04-19 17:36 30M
gc5Base.sql 2010-04-19 17:36 1.7K
gc5Base.txt.gz 2010-04-19 17:37 11M
gap.sql 2010-04-19 17:38 1.5K
gap.txt.gz 2010-04-19 17:38 1.5M
chainMonDom5Link.sql 2010-04-19 17:38 1.5K
chainMonDom5Link.txt.gz 2010-04-19 17:39 205M
chainCanFam2.sql 2010-04-19 17:40 1.6K
chainCanFam2.txt.gz 2010-04-19 17:40 43M
chainCanFam2Link.sql 2010-04-19 17:41 1.5K
chainCanFam2Link.txt.gz 2010-04-19 17:42 459M
netMonDom5.sql 2010-04-19 17:44 2.0K
netMonDom5.txt.gz 2010-04-19 17:44 18M
netCanFam2.sql 2010-04-19 17:45 2.0K
netCanFam2.txt.gz 2010-04-19 17:45 42M
rmsk.sql 2010-04-19 17:46 1.8K
rmsk.txt.gz 2010-04-19 17:46 102M
simpleRepeat.sql 2010-04-19 17:46 1.9K
simpleRepeat.txt.gz 2010-04-19 17:46 13M
chainHg19Link.sql 2010-04-19 17:46 1.5K
chainHg19Link.txt.gz 2010-04-19 17:47 369M
chromInfo.sql 2010-04-19 17:49 1.3K
chromInfo.txt.gz 2010-04-19 17:49 238K
blastHg18KG.sql 2010-04-25 10:12 2.1K
blastHg18KG.txt.gz 2010-04-25 10:12 3.2M
chainFelCat4.sql 2010-08-01 12:23 1.6K
chainFelCat4.txt.gz 2010-08-01 12:23 113M
chainFelCat4Link.sql 2010-08-01 12:23 1.5K
chainFelCat4Link.txt.gz 2010-08-01 12:25 695M
netFelCat4.sql 2010-08-01 12:29 2.0K
netFelCat4.txt.gz 2010-08-01 12:29 54M
tRNAs.sql 2012-03-18 16:22 1.7K
tRNAs.txt.gz 2012-03-18 16:22 43K
cytoBandIdeo.sql 2013-04-28 09:42 1.5K
cytoBandIdeo.txt.gz 2013-04-28 09:42 203K
ucscToINSDC.sql 2013-09-15 08:03 1.4K
ucscToINSDC.txt.gz 2013-09-15 08:03 386K
chainMm10.sql 2013-10-27 09:01 1.7K
chainMm10.txt.gz 2013-10-27 09:01 36M
chainMm10Link.sql 2013-10-27 09:01 1.5K
chainMm10Link.txt.gz 2013-10-27 09:02 401M
netMm10.sql 2013-10-27 09:03 2.1K
netMm10.txt.gz 2013-10-27 09:04 60M
genscan.sql 2013-12-09 17:53 1.7K
genscan.txt.gz 2013-12-09 17:53 3.0M
grp.sql 2014-03-02 03:37 1.3K
grp.txt.gz 2014-03-02 03:37 208
augustusGene.sql 2015-07-26 09:45 1.9K
augustusGene.txt.gz 2015-07-26 09:45 2.2M
microsat.sql 2015-08-23 09:14 1.5K
microsat.txt.gz 2015-08-23 09:14 120K
chainRn6.sql 2017-03-26 11:20 1.7K
chainRn6.txt.gz 2017-03-26 11:20 48M
chainRn6Link.sql 2017-03-26 11:21 1.5K
chainRn6Link.txt.gz 2017-03-26 11:28 455M
netRn6.sql 2017-03-26 11:41 2.1K
netRn6.txt.gz 2017-03-26 11:43 60M
chromAlias.sql 2018-02-18 04:57 1.4K
chromAlias.txt.gz 2018-02-18 04:57 672K
ucscToRefSeq.sql 2018-02-18 04:57 1.4K
ucscToRefSeq.txt.gz 2018-02-18 04:57 405K
all_est.sql 2018-04-29 05:34 2.1K
all_est.txt.gz 2018-04-29 05:34 154
estOrientInfo.sql 2018-04-29 05:34 1.8K
estOrientInfo.txt.gz 2018-04-29 05:34 102
mrnaOrientInfo.sql 2020-03-01 04:40 1.8K
all_mrna.sql 2020-03-01 04:40 2.1K
all_mrna.txt.gz 2020-03-01 04:40 11K
mrnaOrientInfo.txt.gz 2020-03-01 04:40 3.1K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.6M
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 245K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 7.4K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.2M
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.5M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.6M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.1M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 617K
xenoMrna.sql 2020-08-18 00:53 2.1K
xenoMrna.txt.gz 2020-08-18 00:53 348M
xenoRefGene.sql 2020-08-18 00:58 2.0K
xenoRefGene.txt.gz 2020-08-18 00:58 34M
xenoRefFlat.sql 2020-08-18 00:58 1.7K
xenoRefFlat.txt.gz 2020-08-18 00:58 31M
xenoRefSeqAli.sql 2020-08-18 01:11 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 01:11 34M
gbLoaded.sql 2020-08-18 01:13 1.6K
gbLoaded.txt.gz 2020-08-18 01:13 18K
ensGene.sql 2020-08-31 15:11 1.9K
ensGene.txt.gz 2020-08-31 15:11 1.9M
ensGtp.sql 2020-08-31 15:11 1.4K
ensGtp.txt.gz 2020-08-31 15:11 235K
ensemblToGeneName.sql 2020-08-31 15:11 1.4K
ensemblToGeneName.txt.gz 2020-08-31 15:11 128K
ensemblSource.sql 2020-08-31 15:38 1.4K
ensemblSource.txt.gz 2020-08-31 15:38 66K
ensPep.sql 2020-08-31 15:39 1.3K
ensPep.txt.gz 2020-08-31 15:39 6.0M
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 31K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 31K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.3K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.3K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.8K
tableList.sql 2024-04-14 03:07 1.6K
tableList.txt.gz 2024-04-14 03:07 3.9K
bigFiles.sql 2024-04-14 03:07 1.4K
bigFiles.txt.gz 2024-04-14 03:07 73