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 - chainFelCat4Link.txt.gz 2010-08-01 12:25 695M chainCanFam2Link.txt.gz 2010-04-19 17:42 459M chainRn6Link.txt.gz 2017-03-26 11:28 455M chainMm10Link.txt.gz 2013-10-27 09:02 401M chainHg19Link.txt.gz 2010-04-19 17:47 369M xenoMrna.txt.gz 2020-08-18 00:53 348M chainMonDom5Link.txt.gz 2010-04-19 17:39 205M chainFelCat4.txt.gz 2010-08-01 12:23 113M rmsk.txt.gz 2010-04-19 17:46 102M netMm10.txt.gz 2013-10-27 09:04 60M netRn6.txt.gz 2017-03-26 11:43 60M netFelCat4.txt.gz 2010-08-01 12:29 54M netHg19.txt.gz 2010-04-19 17:33 50M chainRn6.txt.gz 2017-03-26 11:20 48M chainCanFam2.txt.gz 2010-04-19 17:40 43M netCanFam2.txt.gz 2010-04-19 17:45 42M chainMm10.txt.gz 2013-10-27 09:01 36M xenoRefGene.txt.gz 2020-08-18 00:58 34M xenoRefSeqAli.txt.gz 2020-08-18 01:11 34M xenoRefFlat.txt.gz 2020-08-18 00:58 31M chainMonDom5.txt.gz 2010-04-19 17:36 30M netMonDom5.txt.gz 2010-04-19 17:44 18M simpleRepeat.txt.gz 2010-04-19 17:46 13M chainHg19.txt.gz 2010-04-19 17:33 13M nestedRepeats.txt.gz 2010-04-19 17:33 11M gc5Base.txt.gz 2010-04-19 17:37 11M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 8.5M ensPep.txt.gz 2020-08-31 15:39 6.0M blastHg18KG.txt.gz 2010-04-25 10:12 3.2M ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.1M genscan.txt.gz 2013-12-09 17:53 3.0M ncbiRefSeq.txt.gz 2020-05-10 03:26 2.6M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.6M gold.txt.gz 2010-04-19 17:36 2.4M augustusGene.txt.gz 2015-07-26 09:45 2.2M ensGene.txt.gz 2020-08-31 15:11 1.9M gap.txt.gz 2010-04-19 17:38 1.5M ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.2M chromAlias.txt.gz 2018-02-18 04:57 672K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 617K ucscToRefSeq.txt.gz 2018-02-18 04:57 405K ucscToINSDC.txt.gz 2013-09-15 08:03 386K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 245K chromInfo.txt.gz 2010-04-19 17:49 238K ensGtp.txt.gz 2020-08-31 15:11 235K cytoBandIdeo.txt.gz 2013-04-28 09:42 203K ensemblToGeneName.txt.gz 2020-08-31 15:11 128K microsat.txt.gz 2015-08-23 09:14 120K ensemblSource.txt.gz 2020-08-31 15:38 66K tRNAs.txt.gz 2012-03-18 16:22 43K trackDb.txt.gz 2021-12-27 12:23 41K gbLoaded.txt.gz 2020-08-18 01:13 18K all_mrna.txt.gz 2020-03-01 04:40 11K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 7.4K tableDescriptions.txt.gz 2020-04-26 03:23 6.7K tableList.txt.gz 2022-10-02 03:04 3.8K mrnaOrientInfo.txt.gz 2020-03-01 04:40 3.1K xenoRefSeqAli.sql 2020-08-18 01:11 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K xenoMrna.sql 2020-08-18 00:53 2.1K all_mrna.sql 2020-03-01 04:40 2.1K all_est.sql 2018-04-29 05:34 2.1K netMm10.sql 2013-10-27 09:03 2.1K netRn6.sql 2017-03-26 11:41 2.1K trackDb.sql 2021-12-27 12:23 2.1K blastHg18KG.sql 2010-04-25 10:12 2.1K netMonDom5.sql 2010-04-19 17:44 2.0K netFelCat4.sql 2010-08-01 12:29 2.0K netCanFam2.sql 2010-04-19 17:45 2.0K netHg19.sql 2010-04-19 17:33 2.0K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K augustusGene.sql 2015-07-26 09:45 1.9K xenoRefGene.sql 2020-08-18 00:58 1.9K ncbiRefSeq.sql 2020-05-10 03:26 1.9K ensGene.sql 2020-08-31 15:11 1.9K nestedRepeats.sql 2010-04-19 17:33 1.9K simpleRepeat.sql 2010-04-19 17:46 1.9K rmsk.sql 2010-04-19 17:46 1.8K mrnaOrientInfo.sql 2020-03-01 04:40 1.8K estOrientInfo.sql 2018-04-29 05:34 1.8K hgFindSpec.sql 2021-12-27 12:23 1.8K xenoRefFlat.sql 2020-08-18 00:58 1.7K chainMm10.sql 2013-10-27 09:01 1.7K chainRn6.sql 2017-03-26 11:20 1.7K gc5Base.sql 2010-04-19 17:36 1.7K tRNAs.sql 2012-03-18 16:22 1.7K genscan.sql 2013-12-09 17:53 1.7K chainMonDom5.sql 2010-04-19 17:36 1.6K chainFelCat4.sql 2010-08-01 12:23 1.6K chainCanFam2.sql 2010-04-19 17:40 1.6K chainHg19.sql 2010-04-19 17:33 1.6K gold.sql 2010-04-19 17:36 1.6K gbLoaded.sql 2020-08-18 01:13 1.6K tableList.sql 2022-10-02 03:04 1.6K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K chainMm10Link.sql 2013-10-27 09:01 1.5K chainRn6Link.sql 2017-03-26 11:21 1.5K gap.sql 2010-04-19 17:38 1.5K cytoBandIdeo.sql 2013-04-28 09:42 1.5K history.sql 2010-04-19 17:33 1.5K microsat.sql 2015-08-23 09:14 1.5K chainMonDom5Link.sql 2010-04-19 17:38 1.5K chainFelCat4Link.sql 2010-08-01 12:23 1.5K chainCanFam2Link.sql 2010-04-19 17:41 1.5K chainHg19Link.sql 2010-04-19 17:46 1.5K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K ucscToRefSeq.sql 2018-02-18 04:57 1.4K ucscToINSDC.sql 2013-09-15 08:03 1.4K chromAlias.sql 2018-02-18 04:57 1.4K ensGtp.sql 2020-08-31 15:11 1.4K tableDescriptions.sql 2020-04-26 03:23 1.4K ensemblToGeneName.sql 2020-08-31 15:11 1.4K bigFiles.sql 2022-10-02 03:04 1.4K ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ensemblSource.sql 2020-08-31 15:38 1.4K grp.sql 2014-03-02 03:37 1.3K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ensPep.sql 2020-08-31 15:39 1.3K chromInfo.sql 2010-04-19 17:49 1.3K ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K hgFindSpec.txt.gz 2021-12-27 12:23 1.2K history.txt.gz 2010-04-19 17:33 520 grp.txt.gz 2014-03-02 03:37 208 all_est.txt.gz 2018-04-29 05:34 154 estOrientInfo.txt.gz 2018-04-29 05:34 102 extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 bigFiles.txt.gz 2022-10-02 03:04 73