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 - gc5BaseBw.sql 2011-11-02 16:12 1.2K gc5BaseBw.txt.gz 2011-11-02 16:12 63 nestedRepeats.sql 2011-11-02 16:12 1.9K nestedRepeats.txt.gz 2011-11-02 16:12 363K cpgIslandExt.sql 2011-11-02 16:12 1.6K cpgIslandExt.txt.gz 2011-11-02 16:12 292K netMonDom5.sql 2011-11-02 16:12 2.0K netMonDom5.txt.gz 2011-11-02 16:12 6.9M simpleRepeat.sql 2011-11-02 16:13 1.9K simpleRepeat.txt.gz 2011-11-02 16:13 3.2M chainRn4.sql 2011-11-02 16:13 1.6K ctgPos2.sql 2011-11-02 16:13 1.5K ctgPos2.txt.gz 2011-11-02 16:13 255K chainRn4.txt.gz 2011-11-02 16:13 3.5M chainXenTro3Link.sql 2011-11-02 16:13 1.5K chainXenTro3Link.txt.gz 2011-11-02 16:13 26M chainHg19.sql 2011-11-02 16:13 1.6K chainHg19.txt.gz 2011-11-02 16:13 5.0M netRn4.sql 2011-11-02 16:13 2.0K netRn4.txt.gz 2011-11-02 16:13 5.7M netGalGal3.sql 2011-11-02 16:13 2.0K netGalGal3.txt.gz 2011-11-02 16:14 12M rmsk.sql 2011-11-02 16:15 1.8K rmsk.txt.gz 2011-11-02 16:15 9.2M gap.sql 2011-11-02 16:15 1.5K gap.txt.gz 2011-11-02 16:15 1.8M chainXenTro3.sql 2011-11-02 16:15 1.6K chainXenTro3.txt.gz 2011-11-02 16:15 4.2M netDanRer7.sql 2011-11-02 16:15 2.0K netDanRer7.txt.gz 2011-11-02 16:15 3.7M 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 blastHg18KG.sql 2011-11-02 16:17 2.1K blastHg18KG.txt.gz 2011-11-02 16:17 2.5M chainMonDom5Link.sql 2011-11-02 16:18 1.5K chainMonDom5Link.txt.gz 2011-11-02 16:19 35M chainGalGal3Link.sql 2011-11-02 16:20 1.5K chainGalGal3Link.txt.gz 2011-11-02 16:21 203M chainGalGal3.sql 2011-11-02 16:23 1.6K chainGalGal3.txt.gz 2011-11-02 16:23 53M nscanPep.sql 2011-11-02 16:24 1.3K nscanPep.txt.gz 2011-11-02 16:24 111M nscanGene.sql 2011-11-02 16:27 1.9K nscanGene.txt.gz 2011-11-02 16:27 1.4M gold.sql 2011-11-02 16:29 1.6K gold.txt.gz 2011-11-02 16:29 2.7M netXenTro3.sql 2011-11-02 16:29 2.0K netXenTro3.txt.gz 2011-11-02 16:29 5.1M chainHg19Link.sql 2011-11-02 16:29 1.5K chainHg19Link.txt.gz 2011-11-02 16:29 29M history.sql 2011-11-02 16:31 1.5K history.txt.gz 2011-11-02 16:31 896 chromInfo.sql 2011-11-02 16:31 1.3K chromInfo.txt.gz 2011-11-02 16:31 29K chainMonDom5.sql 2011-11-02 16:38 1.6K chainMonDom5.txt.gz 2011-11-02 16:38 7.9M netHg19.sql 2011-11-02 16:38 2.0K netHg19.txt.gz 2011-11-02 16:38 6.6M chainRn4Link.sql 2011-11-02 16:38 1.5K chainRn4Link.txt.gz 2011-11-02 16:38 23M tRNAs.sql 2012-04-16 02:18 1.7K tRNAs.txt.gz 2012-04-16 02:18 4.7K 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 netGeoFor1.sql 2012-08-19 14:06 2.1K netGeoFor1.txt.gz 2012-08-19 14:06 31M cytoBandIdeo.sql 2013-04-28 18:21 1.5K cytoBandIdeo.txt.gz 2013-04-28 18:21 30K ucscToINSDC.sql 2013-09-15 16:00 1.4K ucscToINSDC.txt.gz 2013-09-15 16:00 43K 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 netMm10.sql 2013-10-27 17:19 2.1K netMm10.txt.gz 2013-10-27 17:19 7.5M genscan.sql 2013-12-10 02:05 1.7K genscan.txt.gz 2013-12-10 02:05 2.2M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 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 netTaeGut2.sql 2014-05-18 22:09 2.1K netTaeGut2.txt.gz 2014-05-18 22:09 29M cpgIslandExtUnmasked.sql 2014-06-01 16:19 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 16:19 298K augustusGene.sql 2015-07-26 16:21 1.9K augustusGene.txt.gz 2015-07-26 16:21 1.5M microsat.sql 2015-08-23 20:58 1.5K microsat.txt.gz 2015-08-23 20:58 17K all_est.sql 2016-07-10 08:36 2.1K all_est.txt.gz 2016-07-10 08:36 652K intronEst.sql 2016-07-10 08:37 2.1K intronEst.txt.gz 2016-07-10 08:37 505K estOrientInfo.sql 2016-07-10 08:37 1.8K estOrientInfo.txt.gz 2016-07-10 08:37 182K all_mrna.sql 2017-01-09 03:07 2.1K all_mrna.txt.gz 2017-01-09 03:07 23K mrnaOrientInfo.sql 2017-01-09 03:07 1.8K mrnaOrientInfo.txt.gz 2017-01-09 03:07 5.7K chromAlias.sql 2018-08-05 08:06 1.4K chromAlias.txt.gz 2018-08-05 08:06 56K xenoMrna.sql 2020-08-22 05:34 2.1K xenoMrna.txt.gz 2020-08-22 05:34 226M xenoRefGene.sql 2020-08-22 05:55 2.0K xenoRefGene.txt.gz 2020-08-22 05:55 26M xenoRefFlat.sql 2020-08-22 05:55 1.7K xenoRefFlat.txt.gz 2020-08-22 05:55 24M xenoRefSeqAli.sql 2020-08-22 05:55 2.1K xenoRefSeqAli.txt.gz 2020-08-22 05:55 23M gbLoaded.sql 2020-08-22 05:55 1.6K gbLoaded.txt.gz 2020-08-22 05:55 41K 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 ensemblToGeneName.sql 2020-08-31 15:41 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:41 94K ensemblSource.sql 2020-08-31 16:02 1.4K ensemblSource.txt.gz 2020-08-31 16:02 51K ensPep.sql 2020-08-31 16:02 1.3K ensPep.txt.gz 2020-08-31 16:02 4.9M trackDb_pushedout.sql 2021-12-27 12:20 2.1K trackDb_pushedout.txt.gz 2021-12-27 12:20 34K hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 1.0K trackDb.sql 2023-03-28 13:50 2.1K trackDb.txt.gz 2023-03-28 13:50 35K hgFindSpec.sql 2023-03-28 13:50 1.8K hgFindSpec.txt.gz 2023-03-28 13:50 1.0K tableDescriptions.sql 2024-04-20 02:03 1.5K tableDescriptions.txt.gz 2024-04-20 02:03 6.0K tableList.sql 2024-04-21 03:36 1.6K tableList.txt.gz 2024-04-21 03:36 4.1K bigFiles.sql 2024-04-21 03:36 1.4K bigFiles.txt.gz 2024-04-21 03:36 68