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