This directory contains a dump of the UCSC genome annotation database for the
Nov. 2014 (Turkey_5.0/melGal5) assembly of the turkey genome
(melGal5, Turkey Genome 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/112
http://www.ncbi.nlm.nih.gov/genome/assembly/226861
http://www.ncbi.nlm.nih.gov/bioproject/62397
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=melGal5
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/melGal5/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/melGal5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/melGal5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal5/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 melGal5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql melGal5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 2017-03-06 16:49 14M
xenoRefSeqAli.sql 2017-03-06 16:49 2.1K
xenoRefGene.txt.gz 2017-03-06 16:49 7.8M
xenoRefGene.sql 2017-03-06 16:49 1.9K
xenoRefFlat.txt.gz 2017-03-06 16:49 7.0M
xenoRefFlat.sql 2017-03-06 16:49 1.7K
windowmaskerSdust.txt.gz 2017-03-06 16:47 54M
windowmaskerSdust.sql 2017-03-06 16:46 1.5K
ucscToRefSeq.txt.gz 2017-03-06 16:46 2.1M
ucscToRefSeq.sql 2017-03-06 16:46 1.4K
ucscToINSDC.txt.gz 2017-03-06 16:46 2.0M
ucscToINSDC.sql 2017-03-06 16:46 1.4K
trackDb.txt.gz 2024-07-25 09:34 73K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-12-29 03:05 4.7K
tableList.sql 2024-12-29 03:05 1.6K
tableDescriptions.txt.gz 2024-12-28 02:09 7.3K
tableDescriptions.sql 2024-12-28 02:09 1.5K
simpleRepeat.txt.gz 2017-03-06 16:45 7.1M
simpleRepeat.sql 2017-03-06 16:45 1.9K
seqNcbiRefSeq.txt.gz 2021-02-10 16:00 590K
seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K
rmsk.txt.gz 2017-03-06 16:45 14M
rmsk.sql 2017-03-06 16:45 1.9K
refSeqAli.txt.gz 2017-03-06 16:45 9.8K
refSeqAli.sql 2017-03-06 16:45 2.1K
refLink.txt.gz 2017-03-06 16:44 11M
refLink.sql 2017-03-06 16:44 1.7K
refGene.txt.gz 2017-03-06 16:44 9.0K
refGene.sql 2017-03-06 16:44 1.9K
refFlat.txt.gz 2017-03-06 16:44 8.1K
refFlat.sql 2017-03-06 16:44 1.7K
netXenTro7.txt.gz 2017-03-06 16:44 4.9M
netXenTro7.sql 2017-03-06 16:44 2.1K
netTaeGut2.txt.gz 2017-03-06 16:43 33M
netTaeGut2.sql 2017-03-06 16:42 2.1K
netRn6.txt.gz 2017-03-06 16:42 6.1M
netRn6.sql 2017-03-06 16:42 2.1K
netMonDom5.txt.gz 2017-03-06 16:42 7.2M
netMonDom5.sql 2017-03-06 16:42 2.1K
netMm10.txt.gz 2017-03-06 16:42 7.8M
netMm10.sql 2017-03-06 16:41 2.1K
netHg38.txt.gz 2017-03-06 16:41 9.5M
netHg38.sql 2017-03-06 16:41 2.1K
netGeoFor1.txt.gz 2017-03-06 16:40 36M
netGeoFor1.sql 2017-03-06 16:39 2.1K
netGalGal6.txt.gz 2019-01-20 20:08 20M
netGalGal6.sql 2019-01-20 20:08 2.1K
netGalGal5.txt.gz 2017-03-06 16:39 17M
netGalGal5.sql 2017-03-06 16:38 2.1K
netFalPer1.txt.gz 2017-03-06 16:37 30M
netFalPer1.sql 2017-03-06 16:37 2.1K
netDanRer10.txt.gz 2017-03-06 16:37 3.8M
netDanRer10.sql 2017-03-06 16:37 2.1K
nestedRepeats.txt.gz 2017-03-06 16:37 460K
nestedRepeats.sql 2017-03-06 16:37 1.9K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:35 2.9M
ncbiRefSeqPsl.sql 2021-02-10 15:35 2.1K
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:35 2.3M
ncbiRefSeqPredicted.sql 2021-02-10 15:35 2.0K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 6.6M
ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K
ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75
ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K
ncbiRefSeqLink.txt.gz 2021-02-10 15:35 1.1M
ncbiRefSeqLink.sql 2021-02-10 15:35 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:35 8.5K
ncbiRefSeqCurated.sql 2021-02-10 15:35 2.0K
ncbiRefSeqCds.txt.gz 2021-02-10 16:00 203K
ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K
ncbiRefSeq.txt.gz 2021-02-10 15:35 2.3M
ncbiRefSeq.sql 2021-02-10 15:35 2.0K
mrnaOrientInfo.txt.gz 2017-03-06 16:37 7.7K
mrnaOrientInfo.sql 2017-03-06 16:37 1.8K
microsat.txt.gz 2017-03-06 16:20 26K
microsat.sql 2017-03-06 16:20 1.5K
intronEst.txt.gz 2017-03-06 16:16 554K
intronEst.sql 2017-03-06 16:16 2.1K
history.txt.gz 2017-03-06 13:48 793
history.sql 2017-03-06 13:48 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2017-03-06 16:37 213
grp.sql 2017-03-06 16:37 1.3K
gold.txt.gz 2017-03-06 16:36 3.7M
gold.sql 2017-03-06 16:36 1.7K
genscan.txt.gz 2017-03-06 16:25 1.7M
genscan.sql 2017-03-06 16:25 1.7K
gc5BaseBw.txt.gz 2017-03-06 16:23 66
gc5BaseBw.sql 2017-03-06 16:23 1.3K
gbStatus.txt.gz 2017-03-06 16:23 3.4M
gbStatus.sql 2017-03-06 16:22 1.9K
gbExtFile.txt.gz 2017-03-06 16:20 768
gbExtFile.sql 2017-03-06 16:20 1.4K
gap.txt.gz 2017-03-06 16:15 774K
gap.sql 2017-03-06 16:15 1.6K
extNcbiRefSeq.txt.gz 2021-02-10 16:00 91
extNcbiRefSeq.sql 2021-02-10 16:00 1.5K
estOrientInfo.txt.gz 2017-03-06 15:45 224K
estOrientInfo.sql 2017-03-06 15:45 1.8K
ensemblToGeneName.txt.gz 2021-06-01 15:42 82K
ensemblToGeneName.sql 2021-06-01 15:42 1.4K
ensemblSource.txt.gz 2021-06-01 15:46 87K
ensemblSource.sql 2021-06-01 15:46 1.4K
ensPep.txt.gz 2021-06-01 15:46 9.8M
ensPep.sql 2021-06-01 15:46 1.3K
ensGtp.txt.gz 2021-06-01 15:42 303K
ensGtp.sql 2021-06-01 15:42 1.4K
ensGene.txt.gz 2021-06-01 15:42 2.0M
ensGene.sql 2021-06-01 15:42 1.9K
cytoBandIdeo.txt.gz 2017-03-06 15:42 1.0M
cytoBandIdeo.sql 2017-03-06 15:42 1.5K
cpgIslandExtUnmasked.txt.gz 2017-03-06 14:35 760K
cpgIslandExtUnmasked.sql 2017-03-06 14:35 1.7K
cpgIslandExt.txt.gz 2017-03-06 14:22 566K
cpgIslandExt.sql 2017-03-06 14:22 1.7K
chromInfo.txt.gz 2017-03-06 13:55 958K
chromInfo.sql 2017-03-06 13:55 1.4K
chromAlias.txt.gz 2018-02-18 07:21 2.7M
chromAlias.sql 2018-02-18 07:21 1.4K
chainXenTro7Link.txt.gz 2017-03-06 13:52 22M
chainXenTro7Link.sql 2017-03-06 13:51 1.5K
chainXenTro7.txt.gz 2017-03-06 16:36 6.5M
chainXenTro7.sql 2017-03-06 16:36 1.7K
chainTaeGut2Link.txt.gz 2017-03-06 16:28 230M
chainTaeGut2Link.sql 2017-03-06 16:25 1.5K
chainTaeGut2.txt.gz 2017-03-06 13:50 21M
chainTaeGut2.sql 2017-03-06 13:50 1.7K
chainRn6Link.txt.gz 2017-03-06 13:49 25M
chainRn6Link.sql 2017-03-06 13:48 1.5K
chainRn6.txt.gz 2017-03-06 13:48 5.4M
chainRn6.sql 2017-03-06 13:48 1.7K
chainMonDom5Link.txt.gz 2017-03-06 16:24 42M
chainMonDom5Link.sql 2017-03-06 16:23 1.5K
chainMonDom5.txt.gz 2017-03-06 16:23 12M
chainMonDom5.sql 2017-03-06 16:23 1.7K
chainMm10Link.txt.gz 2017-03-06 16:21 47M
chainMm10Link.sql 2017-03-06 16:20 1.5K
chainMm10.txt.gz 2017-03-06 16:20 7.4M
chainMm10.sql 2017-03-06 16:20 1.7K
chainHg38Link.txt.gz 2017-03-06 16:17 97M
chainHg38Link.sql 2017-03-06 16:16 1.5K
chainHg38.txt.gz 2017-03-06 16:15 19M
chainHg38.sql 2017-03-06 16:15 1.7K
chainGeoFor1Link.txt.gz 2017-03-06 15:53 643M
chainGeoFor1Link.sql 2017-03-06 15:45 1.5K
chainGeoFor1.txt.gz 2017-03-06 15:43 99M
chainGeoFor1.sql 2017-03-06 15:42 1.7K
chainGalGal6Link.txt.gz 2019-01-20 19:50 4.8G
chainGalGal6Link.sql 2019-01-20 19:44 1.5K
chainGalGal6.txt.gz 2019-01-20 19:41 948M
chainGalGal6.sql 2019-01-20 19:40 1.7K
chainGalGal5Link.txt.gz 2017-03-06 14:54 1.4G
chainGalGal5Link.sql 2017-03-06 14:35 1.5K
chainGalGal5.txt.gz 2017-03-06 14:25 301M
chainGalGal5.sql 2017-03-06 14:22 1.7K
chainFalPer1Link.txt.gz 2017-03-06 14:01 600M
chainFalPer1Link.sql 2017-03-06 13:55 1.5K
chainFalPer1.txt.gz 2017-03-06 13:53 84M
chainFalPer1.sql 2017-03-06 13:52 1.7K
chainDanRer10Link.txt.gz 2017-03-06 13:51 20M
chainDanRer10Link.sql 2017-03-06 13:50 1.6K
chainDanRer10.txt.gz 2017-03-06 13:50 5.8M
chainDanRer10.sql 2017-03-06 13:49 1.7K
bigFiles.txt.gz 2024-12-29 03:05 95
bigFiles.sql 2024-12-29 03:05 1.4K
augustusGene.txt.gz 2017-03-06 13:48 1.6M
augustusGene.sql 2017-03-06 13:48 1.9K
all_mrna.txt.gz 2017-03-06 13:48 25K
all_mrna.sql 2017-03-06 13:48 2.1K
all_est.txt.gz 2017-03-06 13:48 779K
all_est.sql 2017-03-06 13:48 2.1K