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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
chainGalGal6Link.txt.gz 2019-01-20 19:50 4.8G
chainGalGal5Link.txt.gz 2017-03-06 14:54 1.4G
chainGalGal6.txt.gz 2019-01-20 19:41 948M
chainGeoFor1Link.txt.gz 2017-03-06 15:53 643M
chainFalPer1Link.txt.gz 2017-03-06 14:01 600M
chainGalGal5.txt.gz 2017-03-06 14:25 301M
chainTaeGut2Link.txt.gz 2017-03-06 16:28 230M
chainGeoFor1.txt.gz 2017-03-06 15:43 99M
chainHg38Link.txt.gz 2017-03-06 16:17 97M
chainFalPer1.txt.gz 2017-03-06 13:53 84M
windowmaskerSdust.txt.gz 2017-03-06 16:47 54M
chainMm10Link.txt.gz 2017-03-06 16:21 47M
chainMonDom5Link.txt.gz 2017-03-06 16:24 42M
netGeoFor1.txt.gz 2017-03-06 16:40 36M
netTaeGut2.txt.gz 2017-03-06 16:43 33M
netFalPer1.txt.gz 2017-03-06 16:37 30M
chainRn6Link.txt.gz 2017-03-06 13:49 25M
chainXenTro7Link.txt.gz 2017-03-06 13:52 22M
chainTaeGut2.txt.gz 2017-03-06 13:50 21M
netGalGal6.txt.gz 2019-01-20 20:08 20M
chainDanRer10Link.txt.gz 2017-03-06 13:51 20M
chainHg38.txt.gz 2017-03-06 16:15 19M
netGalGal5.txt.gz 2017-03-06 16:39 17M
rmsk.txt.gz 2017-03-06 16:45 14M
xenoRefSeqAli.txt.gz 2017-03-06 16:49 14M
chainMonDom5.txt.gz 2017-03-06 16:23 12M
refLink.txt.gz 2017-03-06 16:44 11M
ensPep.txt.gz 2021-06-01 15:46 9.8M
netHg38.txt.gz 2017-03-06 16:41 9.5M
xenoRefGene.txt.gz 2017-03-06 16:49 7.8M
netMm10.txt.gz 2017-03-06 16:42 7.8M
chainMm10.txt.gz 2017-03-06 16:20 7.4M
netMonDom5.txt.gz 2017-03-06 16:42 7.2M
simpleRepeat.txt.gz 2017-03-06 16:45 7.1M
xenoRefFlat.txt.gz 2017-03-06 16:49 7.0M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 6.6M
chainXenTro7.txt.gz 2017-03-06 16:36 6.5M
netRn6.txt.gz 2017-03-06 16:42 6.1M
chainDanRer10.txt.gz 2017-03-06 13:50 5.8M
chainRn6.txt.gz 2017-03-06 13:48 5.4M
netXenTro7.txt.gz 2017-03-06 16:44 4.9M
netDanRer10.txt.gz 2017-03-06 16:37 3.8M
gold.txt.gz 2017-03-06 16:36 3.7M
gbStatus.txt.gz 2017-03-06 16:23 3.4M
ncbiRefSeqPsl.txt.gz 2021-02-10 15:35 2.9M
chromAlias.txt.gz 2018-02-18 07:21 2.7M
ncbiRefSeq.txt.gz 2021-02-10 15:35 2.3M
ncbiRefSeqPredicted.txt.gz 2021-02-10 15:35 2.3M
ucscToRefSeq.txt.gz 2017-03-06 16:46 2.1M
ensGene.txt.gz 2021-06-01 15:42 2.0M
ucscToINSDC.txt.gz 2017-03-06 16:46 2.0M
genscan.txt.gz 2017-03-06 16:25 1.7M
augustusGene.txt.gz 2017-03-06 13:48 1.6M
ncbiRefSeqLink.txt.gz 2021-02-10 15:35 1.1M
cytoBandIdeo.txt.gz 2017-03-06 15:42 1.0M
chromInfo.txt.gz 2017-03-06 13:55 958K
all_est.txt.gz 2017-03-06 13:48 779K
gap.txt.gz 2017-03-06 16:15 774K
cpgIslandExtUnmasked.txt.gz 2017-03-06 14:35 760K
seqNcbiRefSeq.txt.gz 2021-02-10 16:00 590K
cpgIslandExt.txt.gz 2017-03-06 14:22 566K
intronEst.txt.gz 2017-03-06 16:16 554K
nestedRepeats.txt.gz 2017-03-06 16:37 460K
ensGtp.txt.gz 2021-06-01 15:42 303K
estOrientInfo.txt.gz 2017-03-06 15:45 224K
ncbiRefSeqCds.txt.gz 2021-02-10 16:00 203K
ensemblSource.txt.gz 2021-06-01 15:46 87K
ensemblToGeneName.txt.gz 2021-06-01 15:42 82K
trackDb.txt.gz 2024-01-31 15:13 58K
trackDb_pushedout.txt.gz 2023-12-05 13:50 37K
microsat.txt.gz 2017-03-06 16:20 26K
all_mrna.txt.gz 2017-03-06 13:48 25K
refSeqAli.txt.gz 2017-03-06 16:45 9.8K
refGene.txt.gz 2017-03-06 16:44 9.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:35 8.5K
refFlat.txt.gz 2017-03-06 16:44 8.1K
mrnaOrientInfo.txt.gz 2017-03-06 16:37 7.7K
tableDescriptions.txt.gz 2024-04-27 02:03 7.3K
tableList.txt.gz 2024-04-28 03:07 4.9K
ncbiRefSeqPsl.sql 2021-02-10 15:35 2.1K
xenoRefSeqAli.sql 2017-03-06 16:49 2.1K
refSeqAli.sql 2017-03-06 16:45 2.1K
intronEst.sql 2017-03-06 16:16 2.1K
all_mrna.sql 2017-03-06 13:48 2.1K
all_est.sql 2017-03-06 13:48 2.1K
netDanRer10.sql 2017-03-06 16:37 2.1K
netXenTro7.sql 2017-03-06 16:44 2.1K
netTaeGut2.sql 2017-03-06 16:42 2.1K
netMonDom5.sql 2017-03-06 16:42 2.1K
netGeoFor1.sql 2017-03-06 16:39 2.1K
netGalGal6.sql 2019-01-20 20:08 2.1K
netGalGal5.sql 2017-03-06 16:38 2.1K
netFalPer1.sql 2017-03-06 16:37 2.1K
netMm10.sql 2017-03-06 16:41 2.1K
netHg38.sql 2017-03-06 16:41 2.1K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
netRn6.sql 2017-03-06 16:42 2.1K
trackDb.sql 2024-01-31 15:13 2.1K
ncbiRefSeqLink.sql 2021-02-10 15:35 2.0K
ncbiRefSeqPredicted.sql 2021-02-10 15:35 2.0K
ncbiRefSeqCurated.sql 2021-02-10 15:35 2.0K
ncbiRefSeq.sql 2021-02-10 15:35 2.0K
ensGene.sql 2021-06-01 15:42 1.9K
augustusGene.sql 2017-03-06 13:48 1.9K
xenoRefGene.sql 2017-03-06 16:49 1.9K
nestedRepeats.sql 2017-03-06 16:37 1.9K
simpleRepeat.sql 2017-03-06 16:45 1.9K
refGene.sql 2017-03-06 16:44 1.9K
gbStatus.sql 2017-03-06 16:22 1.9K
rmsk.sql 2017-03-06 16:45 1.9K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
mrnaOrientInfo.sql 2017-03-06 16:37 1.8K
estOrientInfo.sql 2017-03-06 15:45 1.8K
hgFindSpec.sql 2024-01-31 15:13 1.8K
refLink.sql 2017-03-06 16:44 1.7K
xenoRefFlat.sql 2017-03-06 16:49 1.7K
chainDanRer10.sql 2017-03-06 13:49 1.7K
cpgIslandExtUnmasked.sql 2017-03-06 14:35 1.7K
chainXenTro7.sql 2017-03-06 16:36 1.7K
chainTaeGut2.sql 2017-03-06 13:50 1.7K
chainMonDom5.sql 2017-03-06 16:23 1.7K
chainGeoFor1.sql 2017-03-06 15:42 1.7K
chainGalGal6.sql 2019-01-20 19:40 1.7K
chainGalGal5.sql 2017-03-06 14:22 1.7K
chainFalPer1.sql 2017-03-06 13:52 1.7K
refFlat.sql 2017-03-06 16:44 1.7K
chainMm10.sql 2017-03-06 16:20 1.7K
chainHg38.sql 2017-03-06 16:15 1.7K
chainRn6.sql 2017-03-06 13:48 1.7K
cpgIslandExt.sql 2017-03-06 14:22 1.7K
genscan.sql 2017-03-06 16:25 1.7K
gold.sql 2017-03-06 16:36 1.7K
gap.sql 2017-03-06 16:15 1.6K
tableList.sql 2024-04-28 03:07 1.6K
history.sql 2017-03-06 13:48 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K
chainDanRer10Link.sql 2017-03-06 13:50 1.6K
chainXenTro7Link.sql 2017-03-06 13:51 1.5K
chainTaeGut2Link.sql 2017-03-06 16:25 1.5K
chainMonDom5Link.sql 2017-03-06 16:23 1.5K
chainGeoFor1Link.sql 2017-03-06 15:45 1.5K
chainGalGal6Link.sql 2019-01-20 19:44 1.5K
chainGalGal5Link.sql 2017-03-06 14:35 1.5K
chainFalPer1Link.sql 2017-03-06 13:55 1.5K
chainMm10Link.sql 2017-03-06 16:20 1.5K
chainHg38Link.sql 2017-03-06 16:16 1.5K
chainRn6Link.sql 2017-03-06 13:48 1.5K
cytoBandIdeo.sql 2017-03-06 15:42 1.5K
windowmaskerSdust.sql 2017-03-06 16:46 1.5K
microsat.sql 2017-03-06 16:20 1.5K
extNcbiRefSeq.sql 2021-02-10 16:00 1.5K
tableDescriptions.sql 2024-04-27 02:03 1.5K
ensGtp.sql 2021-06-01 15:42 1.4K
ucscToRefSeq.sql 2017-03-06 16:46 1.4K
ucscToINSDC.sql 2017-03-06 16:46 1.4K
chromAlias.sql 2018-02-18 07:21 1.4K
ensemblToGeneName.sql 2021-06-01 15:42 1.4K
bigFiles.sql 2024-04-28 03:07 1.4K
gbExtFile.sql 2017-03-06 16:20 1.4K
chromInfo.sql 2017-03-06 13:55 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K
ensemblSource.sql 2021-06-01 15:46 1.4K
ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K
grp.sql 2017-03-06 16:37 1.3K
ensPep.sql 2021-06-01 15:46 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K
gc5BaseBw.sql 2017-03-06 16:23 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
history.txt.gz 2017-03-06 13:48 793
gbExtFile.txt.gz 2017-03-06 16:20 768
grp.txt.gz 2017-03-06 16:37 213
bigFiles.txt.gz 2024-04-28 03:07 95
extNcbiRefSeq.txt.gz 2021-02-10 16:00 91
ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75
gc5BaseBw.txt.gz 2017-03-06 16:23 66