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 tableDescriptions.sql 2020-04-26 03:23 1.4K tableDescriptions.txt.gz 2020-04-26 03:23 6.7K 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 xenoRefFlat.sql 2020-08-18 00:58 1.7K xenoRefGene.sql 2020-08-18 00:58 1.9K xenoRefGene.txt.gz 2020-08-18 00:58 34M 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 ensemblToGeneName.sql 2020-08-31 15:11 1.4K ensGtp.txt.gz 2020-08-31 15:11 235K 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 2021-12-27 12:23 2.1K trackDb.txt.gz 2021-12-27 12:23 41K hgFindSpec.sql 2021-12-27 12:23 1.8K hgFindSpec.txt.gz 2021-12-27 12:23 1.2K tableList.sql 2022-10-02 03:04 1.6K tableList.txt.gz 2022-10-02 03:04 3.8K bigFiles.sql 2022-10-02 03:04 1.4K bigFiles.txt.gz 2022-10-02 03:04 73