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.
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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.txt.gz 2011-11-02 16:12 63
bigFiles.txt.gz 2024-05-05 03:32 68
grp.txt.gz 2014-03-02 04:14 208
history.txt.gz 2011-11-02 16:31 896
hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 1.0K
hgFindSpec.txt.gz 2023-03-28 13:50 1.0K
gc5BaseBw.sql 2011-11-02 16:12 1.2K
nscanPep.sql 2011-11-02 16:24 1.3K
chromInfo.sql 2011-11-02 16:31 1.3K
ensPep.sql 2020-08-31 16:02 1.3K
grp.sql 2014-03-02 04:14 1.3K
ensemblSource.sql 2020-08-31 16:02 1.4K
bigFiles.sql 2024-05-05 03:32 1.4K
ensemblToGeneName.sql 2020-08-31 15:41 1.4K
chromAlias.sql 2018-08-05 08:06 1.4K
ucscToINSDC.sql 2013-09-15 16:00 1.4K
ensGtp.sql 2020-08-31 15:41 1.4K
tableDescriptions.sql 2024-05-04 02:03 1.5K
chainRn4Link.sql 2011-11-02 16:38 1.5K
chainHg19Link.sql 2011-11-02 16:29 1.5K
ctgPos2.sql 2011-11-02 16:13 1.5K
chainDanRer7Link.sql 2011-11-02 16:17 1.5K
chainGalGal3Link.sql 2011-11-02 16:20 1.5K
chainMonDom5Link.sql 2011-11-02 16:18 1.5K
chainXenTro3Link.sql 2011-11-02 16:13 1.5K
microsat.sql 2015-08-23 20:58 1.5K
history.sql 2011-11-02 16:31 1.5K
cytoBandIdeo.sql 2013-04-28 18:21 1.5K
gap.sql 2011-11-02 16:15 1.5K
chainMm10Link.sql 2013-10-27 17:19 1.5K
chainTaeGut2Link.sql 2014-05-18 22:08 1.5K
chainGeoFor1Link.sql 2012-08-19 14:05 1.6K
tableList.sql 2024-05-05 03:32 1.6K
gold.sql 2011-11-02 16:29 1.6K
gbLoaded.sql 2020-08-22 05:55 1.6K
cpgIslandExt.sql 2011-11-02 16:12 1.6K
chainRn4.sql 2011-11-02 16:13 1.6K
chainHg19.sql 2011-11-02 16:13 1.6K
chainDanRer7.sql 2011-11-02 16:17 1.6K
chainGalGal3.sql 2011-11-02 16:23 1.6K
chainMonDom5.sql 2011-11-02 16:38 1.6K
chainXenTro3.sql 2011-11-02 16:15 1.6K
genscan.sql 2013-12-10 02:05 1.7K
tRNAs.sql 2012-04-16 02:18 1.7K
chainMm10.sql 2013-10-27 17:19 1.7K
chainTaeGut2.sql 2014-05-18 22:08 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 16:19 1.7K
chainGeoFor1.sql 2012-08-19 14:05 1.7K
xenoRefFlat.sql 2020-08-22 05:55 1.7K
hgFindSpec.sql 2023-03-28 13:50 1.8K
estOrientInfo.sql 2016-07-10 08:37 1.8K
mrnaOrientInfo.sql 2017-01-09 03:07 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K
rmsk.sql 2011-11-02 16:15 1.8K
nscanGene.sql 2011-11-02 16:27 1.9K
simpleRepeat.sql 2011-11-02 16:13 1.9K
nestedRepeats.sql 2011-11-02 16:12 1.9K
augustusGene.sql 2015-07-26 16:21 1.9K
ensGene.sql 2020-08-31 15:41 1.9K
xenoRefGene.sql 2020-08-22 05:55 2.0K
netRn4.sql 2011-11-02 16:13 2.0K
netHg19.sql 2011-11-02 16:38 2.0K
netDanRer7.sql 2011-11-02 16:15 2.0K
netGalGal3.sql 2011-11-02 16:13 2.0K
netMonDom5.sql 2011-11-02 16:12 2.0K
netXenTro3.sql 2011-11-02 16:29 2.0K
blastHg18KG.sql 2011-11-02 16:17 2.1K
trackDb.sql 2023-03-28 13:50 2.1K
trackDb_pushedout.sql 2021-12-27 12:20 2.1K
netMm10.sql 2013-10-27 17:19 2.1K
netTaeGut2.sql 2014-05-18 22:09 2.1K
netGeoFor1.sql 2012-08-19 14:06 2.1K
all_est.sql 2016-07-10 08:36 2.1K
all_mrna.sql 2017-01-09 03:07 2.1K
intronEst.sql 2016-07-10 08:37 2.1K
xenoMrna.sql 2020-08-22 05:34 2.1K
xenoRefSeqAli.sql 2020-08-22 05:55 2.1K
tableList.txt.gz 2024-05-05 03:32 4.1K
tRNAs.txt.gz 2012-04-16 02:18 4.7K
mrnaOrientInfo.txt.gz 2017-01-09 03:07 5.7K
tableDescriptions.txt.gz 2024-05-04 02:03 6.0K
microsat.txt.gz 2015-08-23 20:58 17K
all_mrna.txt.gz 2017-01-09 03:07 23K
chromInfo.txt.gz 2011-11-02 16:31 29K
cytoBandIdeo.txt.gz 2013-04-28 18:21 30K
trackDb_pushedout.txt.gz 2021-12-27 12:20 34K
trackDb.txt.gz 2023-03-28 13:50 35K
gbLoaded.txt.gz 2020-08-22 05:55 41K
ucscToINSDC.txt.gz 2013-09-15 16:00 43K
ensemblSource.txt.gz 2020-08-31 16:02 51K
chromAlias.txt.gz 2018-08-05 08:06 56K
ensemblToGeneName.txt.gz 2020-08-31 15:41 94K
ensGtp.txt.gz 2020-08-31 15:41 170K
estOrientInfo.txt.gz 2016-07-10 08:37 182K
ctgPos2.txt.gz 2011-11-02 16:13 255K
cpgIslandExt.txt.gz 2011-11-02 16:12 292K
cpgIslandExtUnmasked.txt.gz 2014-06-01 16:19 298K
nestedRepeats.txt.gz 2011-11-02 16:12 363K
intronEst.txt.gz 2016-07-10 08:37 505K
all_est.txt.gz 2016-07-10 08:36 652K
nscanGene.txt.gz 2011-11-02 16:27 1.4M
augustusGene.txt.gz 2015-07-26 16:21 1.5M
ensGene.txt.gz 2020-08-31 15:41 1.6M
gap.txt.gz 2011-11-02 16:15 1.8M
genscan.txt.gz 2013-12-10 02:05 2.2M
blastHg18KG.txt.gz 2011-11-02 16:17 2.5M
gold.txt.gz 2011-11-02 16:29 2.7M
simpleRepeat.txt.gz 2011-11-02 16:13 3.2M
chainRn4.txt.gz 2011-11-02 16:13 3.5M
netDanRer7.txt.gz 2011-11-02 16:15 3.7M
chainXenTro3.txt.gz 2011-11-02 16:15 4.2M
chainMm10.txt.gz 2013-10-27 17:19 4.7M
ensPep.txt.gz 2020-08-31 16:02 4.9M
chainHg19.txt.gz 2011-11-02 16:13 5.0M
netXenTro3.txt.gz 2011-11-02 16:29 5.1M
chainDanRer7.txt.gz 2011-11-02 16:17 5.3M
netRn4.txt.gz 2011-11-02 16:13 5.7M
netHg19.txt.gz 2011-11-02 16:38 6.6M
netMonDom5.txt.gz 2011-11-02 16:12 6.9M
netMm10.txt.gz 2013-10-27 17:19 7.5M
chainMonDom5.txt.gz 2011-11-02 16:38 7.9M
rmsk.txt.gz 2011-11-02 16:15 9.2M
netGalGal3.txt.gz 2011-11-02 16:14 12M
chainTaeGut2.txt.gz 2014-05-18 22:08 18M
chainDanRer7Link.txt.gz 2011-11-02 16:17 19M
chainRn4Link.txt.gz 2011-11-02 16:38 23M
xenoRefSeqAli.txt.gz 2020-08-22 05:55 23M
xenoRefFlat.txt.gz 2020-08-22 05:55 24M
xenoRefGene.txt.gz 2020-08-22 05:55 26M
chainXenTro3Link.txt.gz 2011-11-02 16:13 26M
chainHg19Link.txt.gz 2011-11-02 16:29 29M
netTaeGut2.txt.gz 2014-05-18 22:09 29M
netGeoFor1.txt.gz 2012-08-19 14:06 31M
chainMonDom5Link.txt.gz 2011-11-02 16:19 35M
chainMm10Link.txt.gz 2013-10-27 17:19 42M
chainGeoFor1.txt.gz 2012-08-19 14:05 42M
chainGalGal3.txt.gz 2011-11-02 16:23 53M
nscanPep.txt.gz 2011-11-02 16:24 111M
chainGalGal3Link.txt.gz 2011-11-02 16:21 203M
chainTaeGut2Link.txt.gz 2014-05-18 22:08 210M
xenoMrna.txt.gz 2020-08-22 05:34 226M
chainGeoFor1Link.txt.gz 2012-08-19 14:05 272M