This directory contains a dump of the UCSC genome annotation database for the
Feb. 2013 (WashU taeGut324/taeGut2) assembly of the zebra finch genome
(taeGut2, Washington University School of Medicine) .
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/367
http://www.ncbi.nlm.nih.gov/genome/assembly/524908
http://www.ncbi.nlm.nih.gov/bioproject/17289
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=taeGut2
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/taeGut2/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/taeGut2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/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 taeGut2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql taeGut2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Zebra finch sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
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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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
all_est.sql 2014-05-08 12:10 2.1K
all_est.txt.gz 2014-05-08 12:10 4.0M
history.sql 2014-05-08 12:10 1.6K
history.txt.gz 2014-05-08 12:10 527K
intronEst.sql 2014-05-08 12:10 2.1K
intronEst.txt.gz 2014-05-08 12:10 2.1M
chainGalGal4.sql 2014-05-08 12:11 1.7K
chainGalGal4.txt.gz 2014-05-08 12:11 17M
chainGalGal4Link.sql 2014-05-08 12:11 1.5K
chainGalGal4Link.txt.gz 2014-05-08 12:11 223M
chainHg19.sql 2014-05-08 12:12 1.7K
chainHg19.txt.gz 2014-05-08 12:12 142M
chainHg19Link.sql 2014-05-08 12:12 1.5K
chainHg19Link.txt.gz 2014-05-08 12:13 400M
chromInfo.sql 2014-05-08 12:16 1.4K
chromInfo.txt.gz 2014-05-08 12:16 201K
cpgIslandExt.sql 2014-05-08 12:16 1.7K
cpgIslandExt.txt.gz 2014-05-08 12:16 573K
cpgIslandExtUnmasked.sql 2014-05-08 12:16 1.7K
cpgIslandExtUnmasked.txt.gz 2014-05-08 12:16 645K
cytoBandIdeo.sql 2014-05-08 12:16 1.5K
cytoBandIdeo.txt.gz 2014-05-08 12:16 197K
gc5BaseBw.sql 2014-05-08 12:16 1.3K
gc5BaseBw.txt.gz 2014-05-08 12:16 66
genscan.sql 2014-05-08 12:16 1.7K
genscan.txt.gz 2014-05-08 12:16 2.9M
gold.sql 2014-05-08 12:16 1.7K
gold.txt.gz 2014-05-08 12:16 1.9M
estOrientInfo.sql 2014-05-08 12:16 1.8K
estOrientInfo.txt.gz 2014-05-08 12:16 1.1M
extFile.sql 2014-05-08 12:16 1.4K
extFile.txt.gz 2014-05-08 12:16 385K
gap.sql 2014-05-08 12:16 1.6K
gap.txt.gz 2014-05-08 12:16 913K
grp.sql 2014-05-08 12:16 1.3K
grp.txt.gz 2014-05-08 12:16 206
nestedRepeats.sql 2014-05-08 12:16 1.9K
nestedRepeats.txt.gz 2014-05-08 12:16 498K
netGalGal4.sql 2014-05-08 12:16 2.1K
netGalGal4.txt.gz 2014-05-08 12:16 38M
netHg19.sql 2014-05-08 12:16 2.1K
netHg19.txt.gz 2014-05-08 12:16 13M
rmsk.sql 2014-05-08 12:16 1.9K
rmsk.txt.gz 2014-05-08 12:16 14M
simpleRepeat.sql 2014-05-08 12:16 1.9K
simpleRepeat.txt.gz 2014-05-08 12:16 9.3M
ucscToINSDC.sql 2014-05-08 12:16 1.4K
ucscToINSDC.txt.gz 2014-05-08 12:16 293K
windowmaskerSdust.sql 2014-05-08 12:16 1.5K
windowmaskerSdust.txt.gz 2014-05-08 12:16 67M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 1.9M
microsat.sql 2015-08-24 02:22 1.5K
microsat.txt.gz 2015-08-24 02:22 38K
chainMelGal5Link.sql 2017-03-21 06:23 1.5K
chainMelGal5Link.txt.gz 2017-03-21 06:24 233M
chainMelGal5.sql 2017-03-21 06:35 1.7K
chainMelGal5.txt.gz 2017-03-21 06:35 20M
netMelGal5.sql 2017-03-21 06:36 2.1K
netMelGal5.txt.gz 2017-03-21 06:36 42M
ncbiRefSeq.sql 2018-02-09 13:48 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:48 1.8M
ncbiRefSeqCurated.sql 2018-02-09 13:48 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:48 75K
ncbiRefSeqPredicted.sql 2018-02-09 13:48 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:48 1.7M
ncbiRefSeqLink.sql 2018-02-09 13:48 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:48 706K
ncbiRefSeqPsl.sql 2018-02-09 13:48 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:48 1.9M
chromAlias.sql 2018-02-18 08:49 1.4K
chromAlias.txt.gz 2018-02-18 08:49 380K
ucscToRefSeq.sql 2018-02-18 08:49 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:49 302K
extNcbiRefSeq.sql 2018-08-14 02:31 1.5K
extNcbiRefSeq.txt.gz 2018-08-14 02:31 90
ncbiRefSeqCds.sql 2018-08-14 02:31 1.4K
ncbiRefSeqCds.txt.gz 2018-08-14 02:31 122K
ncbiRefSeqOther.sql 2018-08-14 02:31 1.3K
ncbiRefSeqOther.txt.gz 2018-08-14 02:31 75
ncbiRefSeqPepTable.sql 2018-08-14 02:31 1.4K
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:31 5.4M
seqNcbiRefSeq.sql 2018-08-14 02:31 1.6K
seqNcbiRefSeq.txt.gz 2018-08-14 02:31 315K
all_mrna.sql 2018-10-21 09:15 2.1K
all_mrna.txt.gz 2018-10-21 09:15 245K
chainGalGal6.sql 2019-01-20 20:21 1.7K
chainGalGal6.txt.gz 2019-01-20 20:21 70M
netGalGal6.sql 2019-01-20 20:21 2.1K
netGalGal6.txt.gz 2019-01-20 20:21 42M
chainGalGal6Link.sql 2019-01-20 20:22 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:22 494M
refGene.sql 2020-08-20 13:02 1.9K
refGene.txt.gz 2020-08-20 13:02 84K
refFlat.sql 2020-08-20 13:02 1.7K
refFlat.txt.gz 2020-08-20 13:02 75K
xenoRefGene.sql 2020-08-20 13:02 2.0K
xenoRefGene.txt.gz 2020-08-20 13:02 23M
xenoRefFlat.sql 2020-08-20 13:02 1.7K
xenoRefFlat.txt.gz 2020-08-20 13:02 21M
mrnaOrientInfo.sql 2020-08-20 13:02 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 13:02 76K
refSeqAli.sql 2020-08-20 13:02 2.1K
refSeqAli.txt.gz 2020-08-20 13:02 89K
xenoRefSeqAli.sql 2020-08-20 13:18 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 13:18 21M
gbLoaded.sql 2020-08-20 13:18 1.6K
gbLoaded.txt.gz 2020-08-20 13:18 62K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 67K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.1K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
tableList.sql 2024-11-17 03:38 1.6K
tableList.txt.gz 2024-11-17 03:38 3.4K
bigFiles.sql 2024-11-17 03:38 1.4K
bigFiles.txt.gz 2024-11-17 03:38 95