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 - gc5BaseBw.txt.gz 2016-09-18 08:19 66 ncbiRefSeqOther.txt.gz 2018-02-09 14:16 75 grcIncidentDb.txt.gz 2018-05-13 05:42 77 extNcbiRefSeq.txt.gz 2018-02-09 14:16 91 bigFiles.txt.gz 2022-08-14 03:04 120 grp.txt.gz 2016-09-18 08:19 213 history.txt.gz 2016-09-18 08:19 816 snp147ExceptionDesc.txt.gz 2017-04-02 19:06 1.0K gc5BaseBw.sql 2016-09-18 08:19 1.3K grcIncidentDb.sql 2018-05-13 05:42 1.3K ncbiRefSeqOther.sql 2018-02-09 14:16 1.3K ensPep.sql 2018-08-05 06:42 1.3K hgFindSpec.txt.gz 2022-05-06 12:33 1.3K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.3K snp147Seq.sql 2017-04-02 19:06 1.3K grp.sql 2016-09-18 08:19 1.3K ensemblSource.sql 2018-08-05 06:42 1.4K ncbiRefSeqCds.sql 2018-02-09 14:16 1.4K bigFiles.sql 2022-08-14 03:04 1.4K ncbiRefSeqPepTable.sql 2018-02-09 14:16 1.4K chromInfo.sql 2016-09-18 08:19 1.4K snp147ExceptionDesc.sql 2017-04-02 19:06 1.4K ensemblToGeneName.sql 2018-08-05 06:43 1.4K ensGtp.sql 2018-08-05 06:42 1.4K chromAlias.sql 2017-09-03 05:25 1.4K tableDescriptions.sql 2021-08-07 06:33 1.4K ucscToINSDC.sql 2016-09-18 08:20 1.4K ucscToRefSeq.sql 2016-09-18 08:20 1.4K extNcbiRefSeq.sql 2018-02-09 14:16 1.5K microsat.sql 2016-09-18 08:19 1.5K windowmaskerSdust.sql 2016-09-18 08:20 1.5K cytoBandIdeo.sql 2016-09-18 08:19 1.5K chainRn6Link.sql 2016-09-18 08:19 1.5K chainHg38Link.sql 2016-09-18 08:17 1.5K chainMm10Link.sql 2016-09-18 08:18 1.5K chainAquChr2Link.sql 2018-04-01 06:28 1.5K chainMelGal5Link.sql 2017-03-19 21:20 1.5K chainXenTro9Link.sql 2017-12-14 10:29 1.5K chainDanRer10Link.sql 2016-09-18 08:17 1.6K tableList.sql 2022-08-14 03:04 1.6K seqNcbiRefSeq.sql 2018-02-09 14:16 1.6K history.sql 2016-09-18 08:19 1.6K gbLoaded.sql 2020-08-21 19:59 1.6K gap.sql 2016-09-18 08:19 1.6K gold.sql 2016-09-18 08:19 1.7K genscan.sql 2016-09-18 08:19 1.7K cpgIslandExt.sql 2016-09-18 08:19 1.7K chainRn6.sql 2016-09-18 08:19 1.7K chainHg38.sql 2016-09-18 08:17 1.7K chainMm10.sql 2016-09-18 08:18 1.7K refFlat.sql 2020-08-21 19:59 1.7K chainAquChr2.sql 2018-04-01 06:28 1.7K chainMelGal5.sql 2017-03-19 21:14 1.7K chainXenTro9.sql 2017-12-14 10:29 1.7K cpgIslandExtUnmasked.sql 2016-09-18 08:19 1.7K chainDanRer10.sql 2016-09-18 08:17 1.7K xenoRefFlat.sql 2020-08-21 19:59 1.7K snp147CodingDbSnp.sql 2017-04-02 19:05 1.7K hgFindSpec.sql 2022-05-06 12:33 1.8K estOrientInfo.sql 2020-05-08 00:49 1.8K mrnaOrientInfo.sql 2020-08-21 19:59 1.8K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K rmsk.sql 2016-09-18 08:20 1.9K ensGene.sql 2018-08-05 06:42 1.9K refGene.sql 2020-08-21 19:59 1.9K simpleRepeat.sql 2016-09-18 08:20 1.9K nestedRepeats.sql 2016-09-18 08:19 1.9K xenoRefGene.sql 2020-08-21 19:59 1.9K augustusGene.sql 2016-09-18 08:17 1.9K ncbiRefSeq.sql 2018-02-09 13:42 2.0K ncbiRefSeqCurated.sql 2018-02-09 13:42 2.0K ncbiRefSeqPredicted.sql 2018-02-09 13:42 2.0K ncbiRefSeqLink.sql 2018-02-09 13:42 2.0K trackDb.sql 2022-05-06 12:33 2.1K trackDb_pushedout.sql 2022-04-26 10:29 2.1K netRn6.sql 2016-09-18 08:20 2.1K netHg38.sql 2016-09-18 08:19 2.1K netMm10.sql 2016-09-18 08:19 2.1K netAquChr2.sql 2018-04-01 06:31 2.1K netMelGal5.sql 2017-03-19 22:25 2.1K netXenTro9.sql 2017-12-14 10:29 2.1K netDanRer10.sql 2016-09-18 08:19 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 19:59 2.1K xenoRefSeqAli.sql 2020-08-21 19:59 2.1K ncbiRefSeqPsl.sql 2018-02-09 13:42 2.1K snp147.sql 2017-04-02 18:42 3.0K snp147Mult.sql 2017-04-02 19:06 3.0K tableList.txt.gz 2022-08-14 03:04 5.1K tableDescriptions.txt.gz 2021-08-07 06:33 7.9K gap.txt.gz 2016-09-18 08:19 18K microsat.txt.gz 2016-09-18 08:19 25K gbLoaded.txt.gz 2020-08-21 19:59 44K trackDb.txt.gz 2022-05-06 12:33 61K trackDb_pushedout.txt.gz 2022-04-26 10:29 62K cytoBandIdeo.txt.gz 2016-09-18 08:19 116K ensemblSource.txt.gz 2018-08-05 06:42 121K chromInfo.txt.gz 2016-09-18 08:19 127K ensemblToGeneName.txt.gz 2018-08-05 06:43 167K ucscToRefSeq.txt.gz 2016-09-18 08:20 180K ucscToINSDC.txt.gz 2016-09-18 08:20 181K chromAlias.txt.gz 2017-09-03 05:25 261K gold.txt.gz 2016-09-18 08:19 286K ncbiRefSeqCds.txt.gz 2018-02-09 14:16 317K ensGtp.txt.gz 2018-08-05 06:42 387K cpgIslandExt.txt.gz 2016-09-18 08:19 536K mrnaOrientInfo.txt.gz 2020-08-21 19:59 590K ncbiRefSeqCurated.txt.gz 2018-02-09 13:42 657K refFlat.txt.gz 2020-08-21 19:59 676K refGene.txt.gz 2020-08-21 19:59 726K cpgIslandExtUnmasked.txt.gz 2016-09-18 08:19 746K refSeqAli.txt.gz 2020-08-21 19:59 755K seqNcbiRefSeq.txt.gz 2018-02-09 14:16 871K snp147Mult.txt.gz 2017-04-02 19:06 1.2M nestedRepeats.txt.gz 2016-09-18 08:19 1.5M ncbiRefSeqLink.txt.gz 2018-02-09 13:42 1.6M genscan.txt.gz 2016-09-18 08:19 1.7M augustusGene.txt.gz 2016-09-18 08:17 1.7M all_mrna.txt.gz 2020-08-21 19:59 2.0M ensGene.txt.gz 2018-08-05 06:42 2.4M ncbiRefSeqPredicted.txt.gz 2018-02-09 13:42 2.6M ncbiRefSeq.txt.gz 2018-02-09 13:42 3.0M ncbiRefSeqPsl.txt.gz 2018-02-09 13:42 4.3M netXenTro9.txt.gz 2017-12-14 10:29 5.5M netDanRer10.txt.gz 2016-09-18 08:19 5.6M chainXenTro9.txt.gz 2017-12-14 10:29 6.8M estOrientInfo.txt.gz 2020-05-08 00:49 8.0M ensPep.txt.gz 2018-08-05 06:42 8.7M chainMm10.txt.gz 2016-09-18 08:18 8.9M netMm10.txt.gz 2016-09-18 08:20 8.9M netRn6.txt.gz 2016-09-18 08:20 9.1M ncbiRefSeqPepTable.txt.gz 2018-02-09 14:16 9.2M netHg38.txt.gz 2016-09-18 08:19 11M snp147CodingDbSnp.txt.gz 2017-04-02 19:05 12M chainDanRer10.txt.gz 2016-09-18 08:17 12M chainRn6.txt.gz 2016-09-18 08:19 14M simpleRepeat.txt.gz 2016-09-18 08:20 17M xenoRefSeqAli.txt.gz 2020-08-21 19:59 20M intronEst.txt.gz 2020-05-08 00:49 21M xenoRefFlat.txt.gz 2020-08-21 19:59 21M netMelGal5.txt.gz 2017-03-19 22:25 21M rmsk.txt.gz 2016-09-18 08:20 22M xenoRefGene.txt.gz 2020-08-21 19:59 23M chainXenTro9Link.txt.gz 2017-12-14 10:29 25M netAquChr2.txt.gz 2018-04-01 06:31 27M chainHg38.txt.gz 2016-09-18 08:17 27M all_est.txt.gz 2020-05-08 00:49 39M windowmaskerSdust.txt.gz 2016-09-18 08:20 53M chainDanRer10Link.txt.gz 2016-09-18 08:17 54M chainAquChr2.txt.gz 2018-04-01 06:28 72M chainMm10Link.txt.gz 2016-09-18 08:18 73M chainRn6Link.txt.gz 2016-09-18 08:19 96M snp147Seq.txt.gz 2017-04-02 19:07 128M chainHg38Link.txt.gz 2016-09-18 08:18 164M xenoMrna.txt.gz 2020-08-21 19:59 188M chainMelGal5.txt.gz 2017-03-19 21:16 309M snp147.txt.gz 2017-04-02 18:52 332M chainAquChr2Link.txt.gz 2018-04-01 06:29 530M chainMelGal5Link.txt.gz 2017-03-19 21:27 1.4G