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