This directory contains a dump of the UCSC genome annotation database for the
Oct. 2014 (aquChr-1.0.2/aquChr2) assembly of the golden eagle genome
(aquChr2, WashU) .
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/32031
http://www.ncbi.nlm.nih.gov/genome/assembly/217061
http://www.ncbi.nlm.nih.gov/bioproject/256103
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=aquChr2
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/aquChr2/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/aquChr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aquChr2/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 aquChr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql aquChr2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Golden eagle 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 -
bigFiles.txt.gz 2024-11-24 03:06 69
bigFiles.sql 2024-11-24 03:06 1.4K
tableList.txt.gz 2024-11-24 03:06 3.2K
tableList.sql 2024-11-24 03:06 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 7.1K
tableDescriptions.sql 2024-11-23 02:03 1.4K
hgFindSpec.txt.gz 2023-03-28 13:46 586
hgFindSpec.sql 2023-03-28 13:46 1.8K
trackDb.txt.gz 2023-03-28 13:46 37K
trackDb.sql 2023-03-28 13:46 2.1K
gbLoaded.txt.gz 2020-08-18 07:06 5.4K
gbLoaded.sql 2020-08-18 07:06 1.6K
xenoRefSeqAli.txt.gz 2020-08-18 07:06 25M
xenoRefSeqAli.sql 2020-08-18 07:06 2.1K
xenoRefFlat.txt.gz 2020-08-18 07:06 26M
xenoRefFlat.sql 2020-08-18 07:06 1.7K
xenoRefGene.txt.gz 2020-08-18 07:06 29M
xenoRefGene.sql 2020-08-18 07:06 2.0K
netGalGal6.txt.gz 2019-01-20 08:06 42M
netGalGal6.sql 2019-01-20 08:06 2.1K
chainGalGal6Link.txt.gz 2019-01-20 07:58 2.0G
chainGalGal6Link.sql 2019-01-20 07:56 1.5K
chainGalGal6.txt.gz 2019-01-20 07:55 321M
chainGalGal6.sql 2019-01-20 07:55 1.7K
windowmaskerSdust.txt.gz 2017-05-11 14:44 65M
windowmaskerSdust.sql 2017-05-11 14:44 1.5K
ucscToRefSeq.txt.gz 2017-05-11 14:44 9.3K
ucscToRefSeq.sql 2017-05-11 14:44 1.4K
ucscToINSDC.txt.gz 2017-05-11 14:44 9.2K
ucscToINSDC.sql 2017-05-11 14:44 1.4K
tissue.txt.gz 2017-05-11 14:44 59
tissue.sql 2017-05-11 14:44 1.4K
source.txt.gz 2017-05-11 14:44 273K
source.sql 2017-05-11 14:44 1.4K
simpleRepeat.txt.gz 2017-05-11 14:44 4.2M
simpleRepeat.sql 2017-05-11 14:44 1.9K
sex.txt.gz 2017-05-11 14:44 39
sex.sql 2017-05-11 14:44 1.4K
rmsk.txt.gz 2017-05-11 14:44 12M
rmsk.sql 2017-05-11 14:44 1.9K
refSeqSummary.txt.gz 2017-05-11 14:44 5.8M
refSeqSummary.sql 2017-05-11 14:44 1.5K
refSeqStatus.txt.gz 2017-05-11 14:44 1.5M
refSeqStatus.sql 2017-05-11 14:44 1.6K
refLink.txt.gz 2017-05-11 14:44 11M
refLink.sql 2017-05-11 14:44 1.7K
productName.txt.gz 2017-05-11 14:44 2.7M
productName.sql 2017-05-11 14:44 1.4K
organism.txt.gz 2017-05-11 14:44 267K
organism.sql 2017-05-11 14:44 1.4K
history.txt.gz 2017-05-11 14:44 655
history.sql 2017-05-11 14:44 1.6K
gbMiscDiff.txt.gz 2017-05-11 14:44 1.5K
gbMiscDiff.sql 2017-05-11 14:44 1.5K
netHg38.txt.gz 2017-05-11 14:44 11M
netHg38.sql 2017-05-11 14:44 2.1K
gap.txt.gz 2017-05-11 14:44 220K
gap.sql 2017-05-11 14:44 1.6K
netGalGal5.txt.gz 2017-05-11 14:44 38M
netGalGal5.sql 2017-05-11 14:44 2.1K
development.txt.gz 2017-05-11 14:44 47
development.sql 2017-05-11 14:44 1.4K
description.txt.gz 2017-05-11 14:44 8.4M
grp.txt.gz 2017-05-11 14:44 213
grp.sql 2017-05-11 14:44 1.3K
gold.txt.gz 2017-05-11 14:44 294K
gold.sql 2017-05-11 14:44 1.7K
description.sql 2017-05-11 14:44 1.4K
cytoBandIdeo.txt.gz 2017-05-11 14:44 6.6K
cytoBandIdeo.sql 2017-05-11 14:44 1.5K
cpgIslandExtUnmasked.txt.gz 2017-05-11 14:44 843K
cpgIslandExtUnmasked.sql 2017-05-11 14:44 1.7K
netMm10.txt.gz 2017-05-11 14:44 8.1M
netMm10.sql 2017-05-11 14:44 2.1K
cpgIslandExt.txt.gz 2017-05-11 14:44 752K
cpgIslandExt.sql 2017-05-11 14:44 1.7K
nestedRepeats.txt.gz 2017-05-11 14:44 404K
nestedRepeats.sql 2017-05-11 14:44 1.9K
genscan.txt.gz 2017-05-11 14:44 1.6M
genscan.sql 2017-05-11 14:44 1.7K
geneName.txt.gz 2017-05-11 14:44 2.3M
chromInfo.txt.gz 2017-05-11 14:44 7.4K
chromInfo.sql 2017-05-11 14:44 1.4K
chromAlias.txt.gz 2017-05-11 14:44 11K
chromAlias.sql 2017-05-11 14:44 1.4K
geneName.sql 2017-05-11 14:44 1.4K
chainMm10Link.txt.gz 2017-05-11 14:43 55M
gc5BaseBw.txt.gz 2017-05-11 14:43 66
gc5BaseBw.sql 2017-05-11 14:43 1.3K
chainMm10Link.sql 2017-05-11 14:43 1.5K
chainMm10.txt.gz 2017-05-11 14:43 6.4M
mrnaClone.txt.gz 2017-05-11 14:43 1.4K
mrnaClone.sql 2017-05-11 14:43 1.4K
chainMm10.sql 2017-05-11 14:43 1.7K
chainHg38Link.txt.gz 2017-05-11 14:43 139M
gbWarn.txt.gz 2017-05-11 14:43 31
gbWarn.sql 2017-05-11 14:43 1.3K
chainHg38Link.sql 2017-05-11 14:43 1.5K
chainHg38.txt.gz 2017-05-11 14:43 16M
microsat.txt.gz 2017-05-11 14:43 16K
microsat.sql 2017-05-11 14:43 1.5K
chainHg38.sql 2017-05-11 14:43 1.7K
chainGalGal5Link.txt.gz 2017-05-11 14:23 539M
chainGalGal5Link.sql 2017-05-11 14:13 1.5K
gbStatus.txt.gz 2017-05-11 14:13 3.6M
gbStatus.sql 2017-05-11 14:13 1.9K
chainGalGal5.txt.gz 2017-05-11 14:10 70M
chainGalGal5.sql 2017-05-11 14:09 1.7K
gbSeq.txt.gz 2017-05-11 14:09 12M
gbSeq.sql 2017-05-11 14:09 1.7K
library.txt.gz 2017-05-11 14:09 43
library.sql 2017-05-11 14:09 1.4K
gbExtFile.txt.gz 2017-05-11 14:09 1.1K
gbExtFile.sql 2017-05-11 14:09 1.4K
cell.txt.gz 2017-05-11 14:09 40
cell.sql 2017-05-11 14:09 1.4K
cds.txt.gz 2017-05-11 14:08 1.9M
keyword.txt.gz 2017-05-11 14:08 486
keyword.sql 2017-05-11 14:08 1.4K
cds.sql 2017-05-11 14:08 1.4K
imageClone.txt.gz 2017-05-11 14:08 35
imageClone.sql 2017-05-11 14:08 1.5K
author.txt.gz 2017-05-11 14:08 3.1M
author.sql 2017-05-11 14:08 1.4K
augustusGene.txt.gz 2017-05-11 14:08 1.5M
augustusGene.sql 2017-05-11 14:08 1.9K
gbCdnaInfo.txt.gz 2017-05-11 14:08 7.9M
gbCdnaInfo.sql 2017-05-11 14:08 2.6K