This directory contains a dump of the UCSC genome annotation database for
the Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) assembly of the chicken genome (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2))
from the Chicken Genome Sequencing Consortium.
The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/111
    http://www.ncbi.nlm.nih.gov/genome/assembly/317958
    http://www.ncbi.nlm.nih.gov/bioproject/13342

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=galGal4
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/galGal4/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/galGal4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/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 galGal4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galGal4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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The Chicken sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly cited:
   International Chicken Genome Sequencing Consortium.  
   Sequence and comparative analysis of the chicken genome provide unique
   perspectives on vertebrate evolution.
   Nature. 2004 Dec 9;432(7018):695-716.  PMID: 15592404
   See http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. Any redistribution of the data should carry this notice.

All the files and tables in this directory are freely usable for any purpose.

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      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2012-06-11 07:51 63 bigFiles.txt.gz 2023-01-22 03:11 68 grp.txt.gz 2014-03-02 03:41 209 history.txt.gz 2012-06-11 06:20 392 snp138ExceptionDesc.txt.gz 2014-03-09 08:45 1.0K hgFindSpec.txt.gz 2021-12-27 12:19 1.0K gc5BaseBw.sql 2012-06-11 07:51 1.2K chromInfo.sql 2012-06-11 06:21 1.3K ensPep.sql 2015-09-14 02:15 1.3K snp138Seq.sql 2014-03-09 08:45 1.3K grp.sql 2014-03-02 03:41 1.3K ensemblSource.sql 2015-09-14 02:15 1.4K ucscToEnsembl.sql 2013-06-16 17:56 1.4K bigFiles.sql 2023-01-22 03:11 1.4K snp138ExceptionDesc.sql 2014-03-09 08:45 1.4K ensemblToGeneName.sql 2015-09-14 02:15 1.4K tableDescriptions.sql 2019-07-21 03:41 1.4K chromAlias.sql 2018-02-18 06:35 1.4K ucscToINSDC.sql 2013-09-15 13:24 1.4K ucscToRefSeq.sql 2018-02-18 06:35 1.4K ensGtp.sql 2015-09-14 02:14 1.4K windowmaskerSdust.sql 2012-06-11 06:58 1.4K chainMm10Link.sql 2012-06-11 07:47 1.5K microsat.sql 2015-08-23 17:01 1.5K animalQtl.sql 2014-06-29 20:27 1.5K genscanSubopt.sql 2012-06-11 06:20 1.5K history.sql 2012-06-11 06:20 1.5K cytoBandIdeo.sql 2013-04-28 15:31 1.5K gap.sql 2012-06-11 07:11 1.5K chainTaeGut2Link.sql 2014-05-18 18:43 1.5K chainGeoFor1Link.sql 2012-08-19 12:01 1.6K chainPetMar2Link.sql 2013-01-24 00:12 1.6K tableList.sql 2023-01-22 03:11 1.6K gbLoaded.sql 2020-08-21 21:13 1.6K gold.sql 2012-06-11 06:20 1.6K genscan.sql 2012-06-11 06:20 1.6K cpgIslandExt.sql 2012-06-11 06:23 1.6K chainMm10.sql 2012-06-11 07:27 1.6K refFlat.sql 2020-08-21 20:38 1.7K chainTaeGut2.sql 2014-05-18 18:43 1.7K cpgIslandExtUnmasked.sql 2014-06-01 13:30 1.7K chainGeoFor1.sql 2012-08-19 12:04 1.7K chainPetMar2.sql 2013-01-24 00:12 1.7K xenoRefFlat.sql 2020-08-21 20:43 1.7K snp138CodingDbSnp.sql 2014-03-09 08:45 1.7K hgFindSpec.sql 2021-12-27 12:19 1.8K estOrientInfo.sql 2020-05-08 00:49 1.8K mrnaOrientInfo.sql 2020-08-21 20:43 1.8K rmsk.sql 2012-06-11 07:45 1.8K simpleRepeat.sql 2012-06-11 06:21 1.9K nestedRepeats.sql 2012-06-11 07:25 1.9K ensGene.sql 2015-09-14 02:15 1.9K refGene.sql 2020-08-21 20:38 1.9K xenoRefGene.sql 2020-08-21 20:43 1.9K augustusGene.sql 2015-07-26 13:45 1.9K netMm10.sql 2012-06-11 07:08 2.0K trackDb.sql 2021-12-27 12:19 2.1K netTaeGut2.sql 2014-05-18 18:44 2.1K netGeoFor1.sql 2012-08-19 12:01 2.1K netPetMar2.sql 2013-01-24 00:12 2.1K all_est.sql 2020-05-08 00:49 2.1K all_mrna.sql 2020-08-21 19:59 2.1K xenoMrna.sql 2020-08-21 19:59 2.1K intronEst.sql 2020-05-08 00:49 2.1K refSeqAli.sql 2020-08-21 20:58 2.1K xenoRefSeqAli.sql 2020-08-21 20:59 2.1K pubsBingBlatPsl.sql 2014-01-26 12:58 2.2K pubsBingBlat.sql 2014-01-26 12:58 2.4K snp138.sql 2014-03-09 08:44 2.9K snp138Mult.sql 2014-03-09 08:45 2.9K snp138Common.sql 2014-03-09 08:45 3.0K tableList.txt.gz 2023-01-22 03:11 4.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.8K microsat.txt.gz 2015-08-23 17:01 24K animalQtl.txt.gz 2014-06-29 20:27 33K gbLoaded.txt.gz 2020-08-21 21:13 44K ensemblSource.txt.gz 2015-09-14 02:15 56K trackDb.txt.gz 2021-12-27 12:19 57K chromInfo.txt.gz 2012-06-11 06:21 78K cytoBandIdeo.txt.gz 2013-04-28 15:31 79K ucscToEnsembl.txt.gz 2013-06-16 17:56 99K ensemblToGeneName.txt.gz 2015-09-14 02:15 112K ucscToINSDC.txt.gz 2013-09-15 13:24 120K ucscToRefSeq.txt.gz 2018-02-18 06:35 132K chromAlias.txt.gz 2018-02-18 06:35 178K gap.txt.gz 2012-06-11 07:11 181K ensGtp.txt.gz 2015-09-14 02:14 187K gold.txt.gz 2012-06-11 06:20 213K snp138Common.txt.gz 2014-03-09 08:45 383K cpgIslandExt.txt.gz 2012-06-11 06:23 472K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:30 541K mrnaOrientInfo.txt.gz 2020-08-21 20:43 565K refFlat.txt.gz 2020-08-21 20:38 663K pubsBingBlatPsl.txt.gz 2014-01-26 12:58 664K nestedRepeats.txt.gz 2012-06-11 07:25 671K refGene.txt.gz 2020-08-21 20:38 711K refSeqAli.txt.gz 2020-08-21 20:58 753K pubsBingBlat.txt.gz 2014-01-26 12:58 844K genscan.txt.gz 2012-06-11 06:20 1.4M augustusGene.txt.gz 2015-07-26 13:45 1.5M ensGene.txt.gz 2015-09-14 02:15 1.7M all_mrna.txt.gz 2020-08-21 19:59 1.9M netPetMar2.txt.gz 2013-01-24 00:12 2.3M snp138CodingDbSnp.txt.gz 2014-03-09 08:45 2.3M chainPetMar2.txt.gz 2013-01-24 00:12 2.8M genscanSubopt.txt.gz 2012-06-11 06:21 2.8M snp138Mult.txt.gz 2014-03-09 08:45 2.9M simpleRepeat.txt.gz 2012-06-11 06:21 4.9M ensPep.txt.gz 2015-09-14 02:15 5.2M chainMm10.txt.gz 2012-06-11 07:27 7.2M estOrientInfo.txt.gz 2020-05-08 00:49 7.2M netMm10.txt.gz 2012-06-11 07:09 7.7M chainPetMar2Link.txt.gz 2013-01-24 00:12 12M rmsk.txt.gz 2012-06-11 07:45 14M chainTaeGut2.txt.gz 2014-05-18 18:43 18M xenoRefSeqAli.txt.gz 2020-08-21 20:59 19M intronEst.txt.gz 2020-05-08 00:49 19M xenoRefFlat.txt.gz 2020-08-21 20:43 20M xenoRefGene.txt.gz 2020-08-21 20:43 22M netTaeGut2.txt.gz 2014-05-18 18:44 31M netGeoFor1.txt.gz 2012-08-19 12:01 35M all_est.txt.gz 2020-05-08 00:49 36M chainMm10Link.txt.gz 2012-06-11 07:48 53M windowmaskerSdust.txt.gz 2012-06-11 06:59 54M snp138Seq.txt.gz 2014-03-09 08:45 57M chainGeoFor1.txt.gz 2012-08-19 12:04 93M snp138.txt.gz 2014-03-09 08:44 133M xenoMrna.txt.gz 2020-08-21 19:59 173M chainTaeGut2Link.txt.gz 2014-05-18 18:43 222M chainGeoFor1Link.txt.gz 2012-08-19 12:02 589M