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.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.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 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.0K
tableList.sql 2024-12-08 03:33 1.6K
tableList.txt.gz 2024-12-08 03:33 3.9K
bigFiles.sql 2024-12-08 03:33 1.4K
bigFiles.txt.gz 2024-12-08 03:33 68