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