This directory contains a dump of the UCSC genome annotation database for the
    Dec 2015 (Gallus_gallus-5.0/galGal5) assembly of the chicken genome
    (galGal5, International Chicken Genome Consortium) 
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/595851
    http://www.ncbi.nlm.nih.gov/bioproject/10808

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=galGal5
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/galGal5/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/galGal5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/galGal5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal5/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal5/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 galGal5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galGal5 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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 acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

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

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2020-05-08 00:49 2.1K all_est.txt.gz 2020-05-08 00:49 39M all_mrna.sql 2020-08-21 19:59 2.1K all_mrna.txt.gz 2020-08-21 19:59 2.0M augustusGene.sql 2016-09-18 08:17 1.9K augustusGene.txt.gz 2016-09-18 08:17 1.7M bigFiles.sql 2021-05-16 03:03 1.4K bigFiles.txt.gz 2021-05-16 03:03 95 chainAquChr2.sql 2018-04-01 06:28 1.7K chainAquChr2.txt.gz 2018-04-01 06:28 72M chainAquChr2Link.sql 2018-04-01 06:28 1.5K chainAquChr2Link.txt.gz 2018-04-01 06:29 530M chainDanRer10.sql 2016-09-18 08:17 1.7K chainDanRer10.txt.gz 2016-09-18 08:17 12M chainDanRer10Link.sql 2016-09-18 08:17 1.6K chainDanRer10Link.txt.gz 2016-09-18 08:17 54M chainHg38.sql 2016-09-18 08:17 1.7K chainHg38.txt.gz 2016-09-18 08:17 27M chainHg38Link.sql 2016-09-18 08:17 1.5K chainHg38Link.txt.gz 2016-09-18 08:18 164M chainMelGal5.sql 2017-03-19 21:14 1.7K chainMelGal5.txt.gz 2017-03-19 21:16 309M chainMelGal5Link.sql 2017-03-19 21:20 1.5K chainMelGal5Link.txt.gz 2017-03-19 21:27 1.4G chainMm10.sql 2016-09-18 08:18 1.7K chainMm10.txt.gz 2016-09-18 08:18 8.9M chainMm10Link.sql 2016-09-18 08:18 1.5K chainMm10Link.txt.gz 2016-09-18 08:18 73M chainRn6.sql 2016-09-18 08:19 1.7K chainRn6.txt.gz 2016-09-18 08:19 14M chainRn6Link.sql 2016-09-18 08:19 1.5K chainRn6Link.txt.gz 2016-09-18 08:19 96M chainXenTro9.sql 2017-12-14 10:29 1.7K chainXenTro9.txt.gz 2017-12-14 10:29 6.8M chainXenTro9Link.sql 2017-12-14 10:29 1.5K chainXenTro9Link.txt.gz 2017-12-14 10:29 25M chromAlias.sql 2017-09-03 05:25 1.4K chromAlias.txt.gz 2017-09-03 05:25 261K chromInfo.sql 2016-09-18 08:19 1.4K chromInfo.txt.gz 2016-09-18 08:19 127K cpgIslandExt.sql 2016-09-18 08:19 1.7K cpgIslandExt.txt.gz 2016-09-18 08:19 536K cpgIslandExtUnmasked.sql 2016-09-18 08:19 1.7K cpgIslandExtUnmasked.txt.gz 2016-09-18 08:19 746K cytoBandIdeo.sql 2016-09-18 08:19 1.5K cytoBandIdeo.txt.gz 2016-09-18 08:19 116K ensGene.sql 2018-08-05 06:42 1.9K ensGene.txt.gz 2018-08-05 06:42 2.4M ensGtp.sql 2018-08-05 06:42 1.4K ensGtp.txt.gz 2018-08-05 06:42 387K ensPep.sql 2018-08-05 06:42 1.3K ensPep.txt.gz 2018-08-05 06:42 8.7M ensemblSource.sql 2018-08-05 06:42 1.4K ensemblSource.txt.gz 2018-08-05 06:42 121K ensemblToGeneName.sql 2018-08-05 06:43 1.4K ensemblToGeneName.txt.gz 2018-08-05 06:43 167K estOrientInfo.sql 2020-05-08 00:49 1.8K estOrientInfo.txt.gz 2020-05-08 00:49 8.0M gap.sql 2016-09-18 08:19 1.6K gap.txt.gz 2016-09-18 08:19 18K gbLoaded.sql 2020-08-21 19:59 1.6K gbLoaded.txt.gz 2020-08-21 19:59 44K gc5BaseBw.sql 2016-09-18 08:19 1.3K gc5BaseBw.txt.gz 2016-09-18 08:19 66 genscan.sql 2016-09-18 08:19 1.7K genscan.txt.gz 2016-09-18 08:19 1.7M gold.sql 2016-09-18 08:19 1.7K gold.txt.gz 2016-09-18 08:19 286K grcIncidentDb.sql 2018-05-13 05:42 1.3K grcIncidentDb.txt.gz 2018-05-13 05:42 77 grp.sql 2016-09-18 08:19 1.3K grp.txt.gz 2016-09-18 08:19 213 hgFindSpec.sql 2021-01-21 09:35 1.8K hgFindSpec.txt.gz 2021-01-21 09:35 924 history.sql 2016-09-18 08:19 1.6K history.txt.gz 2016-09-18 08:19 816 intronEst.sql 2020-05-08 00:49 2.1K intronEst.txt.gz 2020-05-08 00:49 21M microsat.sql 2016-09-18 08:19 1.5K microsat.txt.gz 2016-09-18 08:19 25K mrnaOrientInfo.sql 2020-08-21 19:59 1.8K mrnaOrientInfo.txt.gz 2020-08-21 19:59 590K nestedRepeats.sql 2016-09-18 08:19 1.9K nestedRepeats.txt.gz 2016-09-18 08:19 1.5M netAquChr2.sql 2018-04-01 06:31 2.1K netAquChr2.txt.gz 2018-04-01 06:31 27M netDanRer10.sql 2016-09-18 08:19 2.1K netDanRer10.txt.gz 2016-09-18 08:19 5.6M netHg38.sql 2016-09-18 08:19 2.1K netHg38.txt.gz 2016-09-18 08:19 11M netMelGal5.sql 2017-03-19 22:25 2.1K netMelGal5.txt.gz 2017-03-19 22:25 21M netMm10.sql 2016-09-18 08:19 2.1K netMm10.txt.gz 2016-09-18 08:20 8.9M netRn6.sql 2016-09-18 08:20 2.1K netRn6.txt.gz 2016-09-18 08:20 9.1M netXenTro9.sql 2017-12-14 10:29 2.1K netXenTro9.txt.gz 2017-12-14 10:29 5.5M refFlat.sql 2020-08-21 19:59 1.7K refFlat.txt.gz 2020-08-21 19:59 676K refGene.sql 2020-08-21 19:59 1.9K refGene.txt.gz 2020-08-21 19:59 726K refSeqAli.sql 2020-08-21 19:59 2.1K refSeqAli.txt.gz 2020-08-21 19:59 755K rmsk.sql 2016-09-18 08:20 1.9K rmsk.txt.gz 2016-09-18 08:20 22M simpleRepeat.sql 2016-09-18 08:20 1.9K simpleRepeat.txt.gz 2016-09-18 08:20 17M snp147.sql 2017-04-02 18:42 3.0K snp147.txt.gz 2017-04-02 18:52 332M snp147CodingDbSnp.sql 2017-04-02 19:05 1.7K snp147CodingDbSnp.txt.gz 2017-04-02 19:05 12M snp147ExceptionDesc.sql 2017-04-02 19:06 1.4K snp147ExceptionDesc.txt.gz 2017-04-02 19:06 1.0K snp147Mult.sql 2017-04-02 19:06 3.0K snp147Mult.txt.gz 2017-04-02 19:06 1.2M snp147Seq.sql 2017-04-02 19:06 1.3K snp147Seq.txt.gz 2017-04-02 19:07 128M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.0K tableList.sql 2021-05-16 03:03 1.6K tableList.txt.gz 2021-05-16 03:03 4.4K trackDb.sql 2021-01-21 09:35 2.1K trackDb.txt.gz 2021-01-21 09:35 56K ucscToINSDC.sql 2016-09-18 08:20 1.4K ucscToINSDC.txt.gz 2016-09-18 08:20 181K ucscToRefSeq.sql 2016-09-18 08:20 1.4K ucscToRefSeq.txt.gz 2016-09-18 08:20 180K windowmaskerSdust.sql 2016-09-18 08:20 1.5K windowmaskerSdust.txt.gz 2016-09-18 08:20 53M xenoMrna.sql 2020-08-21 19:59 2.1K xenoMrna.txt.gz 2020-08-21 19:59 188M xenoRefFlat.sql 2020-08-21 19:59 1.7K xenoRefFlat.txt.gz 2020-08-21 19:59 21M xenoRefGene.sql 2020-08-21 19:59 1.9K xenoRefGene.txt.gz 2020-08-21 19:59 23M xenoRefSeqAli.sql 2020-08-21 19:59 2.1K xenoRefSeqAli.txt.gz 2020-08-21 19:59 20M