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.
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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/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 -
bigFiles.txt.gz 2024-11-24 03:06 73
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
estOrientInfo.txt.gz 2018-04-29 05:34 102
all_est.txt.gz 2018-04-29 05:34 154
grp.txt.gz 2014-03-02 03:37 208
history.txt.gz 2010-04-19 17:33 520
hgFindSpec.txt.gz 2023-12-05 13:50 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
chromInfo.sql 2010-04-19 17:49 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ensPep.sql 2020-08-31 15:39 1.3K
grp.sql 2014-03-02 03:37 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ensemblSource.sql 2020-08-31 15:38 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ensemblToGeneName.sql 2020-08-31 15:11 1.4K
chromAlias.sql 2018-02-18 04:57 1.4K
ucscToINSDC.sql 2013-09-15 08:03 1.4K
ucscToRefSeq.sql 2018-02-18 04:57 1.4K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
ensGtp.sql 2020-08-31 15:11 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.5K
chainHg19Link.sql 2010-04-19 17:46 1.5K
chainCanFam2Link.sql 2010-04-19 17:41 1.5K
chainFelCat4Link.sql 2010-08-01 12:23 1.5K
chainMonDom5Link.sql 2010-04-19 17:38 1.5K
microsat.sql 2015-08-23 09:14 1.5K
history.sql 2010-04-19 17:33 1.5K
cytoBandIdeo.sql 2013-04-28 09:42 1.5K
gap.sql 2010-04-19 17:38 1.5K
chainRn6Link.sql 2017-03-26 11:21 1.5K
chainMm10Link.sql 2013-10-27 09:01 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
tableList.sql 2024-11-24 03:06 1.6K
gold.sql 2010-04-19 17:36 1.6K
gbLoaded.sql 2020-08-18 01:13 1.6K
chainHg19.sql 2010-04-19 17:33 1.6K
chainCanFam2.sql 2010-04-19 17:40 1.6K
chainFelCat4.sql 2010-08-01 12:23 1.6K
chainMonDom5.sql 2010-04-19 17:36 1.6K
genscan.sql 2013-12-09 17:53 1.7K
tRNAs.sql 2012-03-18 16:22 1.7K
gc5Base.sql 2010-04-19 17:36 1.7K
chainRn6.sql 2017-03-26 11:20 1.7K
chainMm10.sql 2013-10-27 09:01 1.7K
xenoRefFlat.sql 2020-08-18 00:58 1.7K
hgFindSpec.sql 2023-12-05 13:50 1.8K
estOrientInfo.sql 2018-04-29 05:34 1.8K
mrnaOrientInfo.sql 2020-03-01 04:40 1.8K
rmsk.sql 2010-04-19 17:46 1.8K
simpleRepeat.sql 2010-04-19 17:46 1.9K
nestedRepeats.sql 2010-04-19 17:33 1.9K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
augustusGene.sql 2015-07-26 09:45 1.9K
ensGene.sql 2020-08-31 15:11 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
xenoRefGene.sql 2020-08-18 00:58 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
netHg19.sql 2010-04-19 17:33 2.0K
netCanFam2.sql 2010-04-19 17:45 2.0K
netFelCat4.sql 2010-08-01 12:29 2.0K
netMonDom5.sql 2010-04-19 17:44 2.0K
blastHg18KG.sql 2010-04-25 10:12 2.1K
trackDb.sql 2023-12-05 13:50 2.1K
netRn6.sql 2017-03-26 11:41 2.1K
netMm10.sql 2013-10-27 09:03 2.1K
all_est.sql 2018-04-29 05:34 2.1K
all_mrna.sql 2020-03-01 04:40 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
xenoMrna.sql 2020-08-18 00:53 2.1K
xenoRefSeqAli.sql 2020-08-18 01:11 2.1K
mrnaOrientInfo.txt.gz 2020-03-01 04:40 3.1K
tableList.txt.gz 2024-11-24 03:06 3.8K
tableDescriptions.txt.gz 2024-11-23 02:03 6.8K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 7.4K
all_mrna.txt.gz 2020-03-01 04:40 11K
gbLoaded.txt.gz 2020-08-18 01:13 18K
trackDb.txt.gz 2023-12-05 13:50 31K
tRNAs.txt.gz 2012-03-18 16:22 43K
ensemblSource.txt.gz 2020-08-31 15:38 66K
microsat.txt.gz 2015-08-23 09:14 120K
ensemblToGeneName.txt.gz 2020-08-31 15:11 128K
cytoBandIdeo.txt.gz 2013-04-28 09:42 203K
ensGtp.txt.gz 2020-08-31 15:11 235K
chromInfo.txt.gz 2010-04-19 17:49 238K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 245K
ucscToINSDC.txt.gz 2013-09-15 08:03 386K
ucscToRefSeq.txt.gz 2018-02-18 04:57 405K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 617K
chromAlias.txt.gz 2018-02-18 04:57 672K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.2M
gap.txt.gz 2010-04-19 17:38 1.5M
ensGene.txt.gz 2020-08-31 15:11 1.9M
augustusGene.txt.gz 2015-07-26 09:45 2.2M
gold.txt.gz 2010-04-19 17:36 2.4M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.6M
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.6M
genscan.txt.gz 2013-12-09 17:53 3.0M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.1M
blastHg18KG.txt.gz 2010-04-25 10:12 3.2M
ensPep.txt.gz 2020-08-31 15:39 6.0M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.5M
gc5Base.txt.gz 2010-04-19 17:37 11M
nestedRepeats.txt.gz 2010-04-19 17:33 11M
chainHg19.txt.gz 2010-04-19 17:33 13M
simpleRepeat.txt.gz 2010-04-19 17:46 13M
netMonDom5.txt.gz 2010-04-19 17:44 18M
chainMonDom5.txt.gz 2010-04-19 17:36 30M
xenoRefFlat.txt.gz 2020-08-18 00:58 31M
xenoRefSeqAli.txt.gz 2020-08-18 01:11 34M
xenoRefGene.txt.gz 2020-08-18 00:58 34M
chainMm10.txt.gz 2013-10-27 09:01 36M
netCanFam2.txt.gz 2010-04-19 17:45 42M
chainCanFam2.txt.gz 2010-04-19 17:40 43M
chainRn6.txt.gz 2017-03-26 11:20 48M
netHg19.txt.gz 2010-04-19 17:33 50M
netFelCat4.txt.gz 2010-08-01 12:29 54M
netRn6.txt.gz 2017-03-26 11:43 60M
netMm10.txt.gz 2013-10-27 09:04 60M
rmsk.txt.gz 2010-04-19 17:46 102M
chainFelCat4.txt.gz 2010-08-01 12:23 113M
chainMonDom5Link.txt.gz 2010-04-19 17:39 205M
xenoMrna.txt.gz 2020-08-18 00:53 348M
chainHg19Link.txt.gz 2010-04-19 17:47 369M
chainMm10Link.txt.gz 2013-10-27 09:02 401M
chainRn6Link.txt.gz 2017-03-26 11:28 455M
chainCanFam2Link.txt.gz 2010-04-19 17:42 459M
chainFelCat4Link.txt.gz 2010-08-01 12:25 695M