This directory contains a dump of the UCSC genome annotation database for
the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly of the turkey genome (melGal1, TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the turkey genome, see the project website:
http://www.ncbi.nlm.nih.gov/genomeprj/10805
http://www.cals.vt.edu/departments/apsc.php

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=melGal1
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/melGal1/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/melGal1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/melGal1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/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 melGal1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql melGal1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'


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

      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-07-10 08:36 2.1K all_est.txt.gz 2016-07-10 08:36 652K all_mrna.sql 2017-01-09 03:07 2.1K all_mrna.txt.gz 2017-01-09 03:07 23K augustusGene.sql 2015-07-26 16:21 1.9K augustusGene.txt.gz 2015-07-26 16:21 1.5M bigFiles.sql 2022-06-26 03:10 1.4K bigFiles.txt.gz 2022-06-26 03:10 68 blastHg18KG.sql 2011-11-02 16:17 2.1K blastHg18KG.txt.gz 2011-11-02 16:17 2.5M chainDanRer7.sql 2011-11-02 16:17 1.6K chainDanRer7.txt.gz 2011-11-02 16:17 5.3M chainDanRer7Link.sql 2011-11-02 16:17 1.5K chainDanRer7Link.txt.gz 2011-11-02 16:17 19M chainGalGal3.sql 2011-11-02 16:23 1.6K chainGalGal3.txt.gz 2011-11-02 16:23 53M chainGalGal3Link.sql 2011-11-02 16:20 1.5K chainGalGal3Link.txt.gz 2011-11-02 16:21 203M chainGeoFor1.sql 2012-08-19 14:05 1.7K chainGeoFor1.txt.gz 2012-08-19 14:05 42M chainGeoFor1Link.sql 2012-08-19 14:05 1.6K chainGeoFor1Link.txt.gz 2012-08-19 14:05 272M chainHg19.sql 2011-11-02 16:13 1.6K chainHg19.txt.gz 2011-11-02 16:13 5.0M chainHg19Link.sql 2011-11-02 16:29 1.5K chainHg19Link.txt.gz 2011-11-02 16:29 29M chainMm10.sql 2013-10-27 17:19 1.7K chainMm10.txt.gz 2013-10-27 17:19 4.7M chainMm10Link.sql 2013-10-27 17:19 1.5K chainMm10Link.txt.gz 2013-10-27 17:19 42M chainMonDom5.sql 2011-11-02 16:38 1.6K chainMonDom5.txt.gz 2011-11-02 16:38 7.9M chainMonDom5Link.sql 2011-11-02 16:18 1.5K chainMonDom5Link.txt.gz 2011-11-02 16:19 35M chainRn4.sql 2011-11-02 16:13 1.6K chainRn4.txt.gz 2011-11-02 16:13 3.5M chainRn4Link.sql 2011-11-02 16:38 1.5K chainRn4Link.txt.gz 2011-11-02 16:38 23M chainTaeGut2.sql 2014-05-18 22:08 1.7K chainTaeGut2.txt.gz 2014-05-18 22:08 18M chainTaeGut2Link.sql 2014-05-18 22:08 1.5K chainTaeGut2Link.txt.gz 2014-05-18 22:08 210M chainXenTro3.sql 2011-11-02 16:15 1.6K chainXenTro3.txt.gz 2011-11-02 16:15 4.2M chainXenTro3Link.sql 2011-11-02 16:13 1.5K chainXenTro3Link.txt.gz 2011-11-02 16:13 26M chromAlias.sql 2018-08-05 08:06 1.4K chromAlias.txt.gz 2018-08-05 08:06 56K chromInfo.sql 2011-11-02 16:31 1.3K chromInfo.txt.gz 2011-11-02 16:31 29K cpgIslandExt.sql 2011-11-02 16:12 1.6K cpgIslandExt.txt.gz 2011-11-02 16:12 292K cpgIslandExtUnmasked.sql 2014-06-01 16:19 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 16:19 298K ctgPos2.sql 2011-11-02 16:13 1.5K ctgPos2.txt.gz 2011-11-02 16:13 255K cytoBandIdeo.sql 2013-04-28 18:21 1.5K cytoBandIdeo.txt.gz 2013-04-28 18:21 30K ensGene.sql 2020-08-31 15:41 1.9K ensGene.txt.gz 2020-08-31 15:41 1.6M ensGtp.sql 2020-08-31 15:41 1.4K ensGtp.txt.gz 2020-08-31 15:41 170K ensPep.sql 2020-08-31 16:02 1.3K ensPep.txt.gz 2020-08-31 16:02 4.9M ensemblSource.sql 2020-08-31 16:02 1.4K ensemblSource.txt.gz 2020-08-31 16:02 51K ensemblToGeneName.sql 2020-08-31 15:41 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:41 94K estOrientInfo.sql 2016-07-10 08:37 1.8K estOrientInfo.txt.gz 2016-07-10 08:37 182K gap.sql 2011-11-02 16:15 1.5K gap.txt.gz 2011-11-02 16:15 1.8M gbLoaded.sql 2020-08-22 05:55 1.6K gbLoaded.txt.gz 2020-08-22 05:55 41K gc5BaseBw.sql 2011-11-02 16:12 1.2K gc5BaseBw.txt.gz 2011-11-02 16:12 63 genscan.sql 2013-12-10 02:05 1.7K genscan.txt.gz 2013-12-10 02:05 2.2M gold.sql 2011-11-02 16:29 1.6K gold.txt.gz 2011-11-02 16:29 2.7M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2021-12-27 12:20 1.8K hgFindSpec.txt.gz 2021-12-27 12:20 1.0K history.sql 2011-11-02 16:31 1.5K history.txt.gz 2011-11-02 16:31 896 intronEst.sql 2016-07-10 08:37 2.1K intronEst.txt.gz 2016-07-10 08:37 505K microsat.sql 2015-08-23 20:58 1.5K microsat.txt.gz 2015-08-23 20:58 17K mrnaOrientInfo.sql 2017-01-09 03:07 1.8K mrnaOrientInfo.txt.gz 2017-01-09 03:07 5.7K nestedRepeats.sql 2011-11-02 16:12 1.9K nestedRepeats.txt.gz 2011-11-02 16:12 363K netDanRer7.sql 2011-11-02 16:15 2.0K netDanRer7.txt.gz 2011-11-02 16:15 3.7M netGalGal3.sql 2011-11-02 16:13 2.0K netGalGal3.txt.gz 2011-11-02 16:14 12M netGeoFor1.sql 2012-08-19 14:06 2.1K netGeoFor1.txt.gz 2012-08-19 14:06 31M netHg19.sql 2011-11-02 16:38 2.0K netHg19.txt.gz 2011-11-02 16:38 6.6M netMm10.sql 2013-10-27 17:19 2.1K netMm10.txt.gz 2013-10-27 17:19 7.5M netMonDom5.sql 2011-11-02 16:12 2.0K netMonDom5.txt.gz 2011-11-02 16:12 6.9M netRn4.sql 2011-11-02 16:13 2.0K netRn4.txt.gz 2011-11-02 16:13 5.7M netTaeGut2.sql 2014-05-18 22:09 2.1K netTaeGut2.txt.gz 2014-05-18 22:09 29M netXenTro3.sql 2011-11-02 16:29 2.0K netXenTro3.txt.gz 2011-11-02 16:29 5.1M nscanGene.sql 2011-11-02 16:27 1.9K nscanGene.txt.gz 2011-11-02 16:27 1.4M nscanPep.sql 2011-11-02 16:24 1.3K nscanPep.txt.gz 2011-11-02 16:24 111M rmsk.sql 2011-11-02 16:15 1.8K rmsk.txt.gz 2011-11-02 16:15 9.2M simpleRepeat.sql 2011-11-02 16:13 1.9K simpleRepeat.txt.gz 2011-11-02 16:13 3.2M tRNAs.sql 2012-04-16 02:18 1.7K tRNAs.txt.gz 2012-04-16 02:18 4.7K tableDescriptions.sql 2019-07-21 03:42 1.4K tableDescriptions.txt.gz 2019-07-21 03:42 6.0K tableList.sql 2022-06-26 03:10 1.6K tableList.txt.gz 2022-06-26 03:10 3.9K trackDb.sql 2021-12-27 12:20 2.1K trackDb.txt.gz 2021-12-27 12:20 34K ucscToINSDC.sql 2013-09-15 16:00 1.4K ucscToINSDC.txt.gz 2013-09-15 16:00 43K xenoMrna.sql 2020-08-22 05:34 2.1K xenoMrna.txt.gz 2020-08-22 05:34 226M xenoRefFlat.sql 2020-08-22 05:55 1.7K xenoRefFlat.txt.gz 2020-08-22 05:55 24M xenoRefGene.sql 2020-08-22 05:55 1.9K xenoRefGene.txt.gz 2020-08-22 05:55 26M xenoRefSeqAli.sql 2020-08-22 05:55 2.1K xenoRefSeqAli.txt.gz 2020-08-22 05:55 23M