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 -
gc5BaseBw.txt.gz 2014-05-08 12:16 66
ncbiRefSeqOther.txt.gz 2018-08-14 02:31 75
extNcbiRefSeq.txt.gz 2018-08-14 02:31 90
bigFiles.txt.gz 2024-04-21 03:38 95
grp.txt.gz 2014-05-08 12:16 206
hgFindSpec.txt.gz 2023-12-05 13:53 1.1K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:53 1.2K
gc5BaseBw.sql 2014-05-08 12:16 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:31 1.3K
grp.sql 2014-05-08 12:16 1.3K
ncbiRefSeqCds.sql 2018-08-14 02:31 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:31 1.4K
chromInfo.sql 2014-05-08 12:16 1.4K
bigFiles.sql 2024-04-21 03:38 1.4K
extFile.sql 2014-05-08 12:16 1.4K
chromAlias.sql 2018-02-18 08:49 1.4K
ucscToINSDC.sql 2014-05-08 12:16 1.4K
ucscToRefSeq.sql 2018-02-18 08:49 1.4K
tableDescriptions.sql 2024-04-20 02:04 1.5K
extNcbiRefSeq.sql 2018-08-14 02:31 1.5K
microsat.sql 2015-08-24 02:22 1.5K
windowmaskerSdust.sql 2014-05-08 12:16 1.5K
cytoBandIdeo.sql 2014-05-08 12:16 1.5K
chainHg19Link.sql 2014-05-08 12:12 1.5K
chainGalGal4Link.sql 2014-05-08 12:11 1.5K
chainGalGal6Link.sql 2019-01-20 20:22 1.5K
chainMelGal5Link.sql 2017-03-21 06:23 1.5K
seqNcbiRefSeq.sql 2018-08-14 02:31 1.6K
history.sql 2014-05-08 12:10 1.6K
tableList.sql 2024-04-21 03:38 1.6K
gap.sql 2014-05-08 12:16 1.6K
gbLoaded.sql 2020-08-20 13:18 1.6K
gold.sql 2014-05-08 12:16 1.7K
genscan.sql 2014-05-08 12:16 1.7K
cpgIslandExt.sql 2014-05-08 12:16 1.7K
chainHg19.sql 2014-05-08 12:12 1.7K
chainGalGal4.sql 2014-05-08 12:11 1.7K
chainGalGal6.sql 2019-01-20 20:21 1.7K
chainMelGal5.sql 2017-03-21 06:35 1.7K
cpgIslandExtUnmasked.sql 2014-05-08 12:16 1.7K
refFlat.sql 2020-08-20 13:02 1.7K
xenoRefFlat.sql 2020-08-20 13:02 1.7K
hgFindSpec.sql 2023-12-05 13:53 1.8K
estOrientInfo.sql 2014-05-08 12:16 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:53 1.8K
mrnaOrientInfo.sql 2020-08-20 13:02 1.8K
rmsk.sql 2014-05-08 12:16 1.9K
simpleRepeat.sql 2014-05-08 12:16 1.9K
nestedRepeats.sql 2014-05-08 12:16 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
refGene.sql 2020-08-20 13:02 1.9K
ncbiRefSeq.sql 2018-02-09 13:48 2.0K
xenoRefGene.sql 2020-08-20 13:02 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:48 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:48 2.0K
ncbiRefSeqLink.sql 2018-02-09 13:48 2.0K
trackDb.sql 2023-12-05 13:53 2.1K
trackDb_pushedout.sql 2023-12-05 13:53 2.1K
netHg19.sql 2014-05-08 12:16 2.1K
netGalGal4.sql 2014-05-08 12:16 2.1K
netGalGal6.sql 2019-01-20 20:21 2.1K
netMelGal5.sql 2017-03-21 06:36 2.1K
all_est.sql 2014-05-08 12:10 2.1K
all_mrna.sql 2018-10-21 09:15 2.1K
intronEst.sql 2014-05-08 12:10 2.1K
refSeqAli.sql 2020-08-20 13:02 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:48 2.1K
xenoRefSeqAli.sql 2020-08-20 13:18 2.1K
tableList.txt.gz 2024-04-21 03:38 3.6K
tableDescriptions.txt.gz 2024-04-20 02:04 6.3K
trackDb.txt.gz 2023-12-05 13:53 33K
trackDb_pushedout.txt.gz 2023-12-05 13:53 33K
microsat.txt.gz 2015-08-24 02:22 38K
gbLoaded.txt.gz 2020-08-20 13:18 62K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:48 75K
refFlat.txt.gz 2020-08-20 13:02 75K
mrnaOrientInfo.txt.gz 2020-08-20 13:02 76K
refGene.txt.gz 2020-08-20 13:02 84K
refSeqAli.txt.gz 2020-08-20 13:02 89K
ncbiRefSeqCds.txt.gz 2018-08-14 02:31 122K
cytoBandIdeo.txt.gz 2014-05-08 12:16 197K
chromInfo.txt.gz 2014-05-08 12:16 201K
all_mrna.txt.gz 2018-10-21 09:15 245K
ucscToINSDC.txt.gz 2014-05-08 12:16 293K
ucscToRefSeq.txt.gz 2018-02-18 08:49 302K
seqNcbiRefSeq.txt.gz 2018-08-14 02:31 315K
chromAlias.txt.gz 2018-02-18 08:49 380K
extFile.txt.gz 2014-05-08 12:16 385K
nestedRepeats.txt.gz 2014-05-08 12:16 498K
history.txt.gz 2014-05-08 12:10 527K
cpgIslandExt.txt.gz 2014-05-08 12:16 573K
cpgIslandExtUnmasked.txt.gz 2014-05-08 12:16 645K
ncbiRefSeqLink.txt.gz 2018-02-09 13:48 706K
gap.txt.gz 2014-05-08 12:16 913K
estOrientInfo.txt.gz 2014-05-08 12:16 1.1M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:48 1.7M
ncbiRefSeq.txt.gz 2018-02-09 13:48 1.8M
gold.txt.gz 2014-05-08 12:16 1.9M
augustusGene.txt.gz 2015-07-26 17:28 1.9M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:48 1.9M
intronEst.txt.gz 2014-05-08 12:10 2.1M
genscan.txt.gz 2014-05-08 12:16 2.9M
all_est.txt.gz 2014-05-08 12:10 4.0M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:31 5.4M
simpleRepeat.txt.gz 2014-05-08 12:16 9.3M
netHg19.txt.gz 2014-05-08 12:16 13M
rmsk.txt.gz 2014-05-08 12:16 14M
chainGalGal4.txt.gz 2014-05-08 12:11 17M
chainMelGal5.txt.gz 2017-03-21 06:35 20M
xenoRefSeqAli.txt.gz 2020-08-20 13:18 21M
xenoRefFlat.txt.gz 2020-08-20 13:02 21M
xenoRefGene.txt.gz 2020-08-20 13:02 23M
netGalGal4.txt.gz 2014-05-08 12:16 38M
netMelGal5.txt.gz 2017-03-21 06:36 42M
netGalGal6.txt.gz 2019-01-20 20:21 42M
windowmaskerSdust.txt.gz 2014-05-08 12:16 67M
chainGalGal6.txt.gz 2019-01-20 20:21 70M
chainHg19.txt.gz 2014-05-08 12:12 142M
chainGalGal4Link.txt.gz 2014-05-08 12:11 223M
chainMelGal5Link.txt.gz 2017-03-21 06:24 233M
chainHg19Link.txt.gz 2014-05-08 12:13 400M
chainGalGal6Link.txt.gz 2019-01-20 20:22 494M