This directory contains a dump of the UCSC genome annotation database for
the Mar. 2011 (Broad/otoGar3) assembly of the bushbaby genome (otoGar3, Broad Institute (GCA_000181295.3)).
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/451
http://www.ncbi.nlm.nih.gov/genome/assembly/249878
http://www.ncbi.nlm.nih.gov/bioproject/16955
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=otoGar3
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/otoGar3/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/otoGar3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/otoGar3/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 otoGar3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql otoGar3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Bushbaby sequence is made freely available before scientific publication
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 particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves 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. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
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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 -
gap.sql 2012-11-21 15:56 1.6K
gap.txt.gz 2012-11-21 15:56 2.6M
chromInfo.sql 2012-11-21 15:56 1.4K
chromInfo.txt.gz 2012-11-21 15:56 33K
nestedRepeats.sql 2012-11-21 15:57 1.9K
nestedRepeats.txt.gz 2012-11-21 15:57 12M
rmsk.sql 2012-11-21 15:57 1.9K
rmsk.txt.gz 2012-11-21 15:57 111M
simpleRepeat.sql 2012-11-21 15:59 1.9K
simpleRepeat.txt.gz 2012-11-21 15:59 13M
cpgIslandExt.sql 2012-11-21 15:59 1.7K
cpgIslandExt.txt.gz 2012-11-21 15:59 463K
netMm10.sql 2012-11-21 15:59 2.1K
netMm10.txt.gz 2012-11-21 16:00 59M
chainMm10.sql 2012-11-21 16:00 1.7K
chainMm10.txt.gz 2012-11-21 16:00 65M
windowmaskerSdust.sql 2012-11-21 16:00 1.5K
windowmaskerSdust.txt.gz 2012-11-21 16:00 124M
chainMm10Link.sql 2012-11-21 16:01 1.5K
chainMm10Link.txt.gz 2012-11-21 16:02 480M
gold.sql 2012-11-21 16:07 1.7K
gold.txt.gz 2012-11-21 16:07 3.3M
genscan.sql 2012-11-21 16:07 1.7K
genscan.txt.gz 2012-11-21 16:07 3.0M
gc5BaseBw.sql 2012-11-21 16:07 1.3K
gc5BaseBw.txt.gz 2012-11-21 16:07 63
history.sql 2012-11-21 16:07 1.6K
history.txt.gz 2012-11-21 16:07 568
cytoBandIdeo.sql 2013-04-28 19:52 1.5K
cytoBandIdeo.txt.gz 2013-04-28 19:52 29K
ucscToINSDC.sql 2013-09-15 17:34 1.4K
ucscToINSDC.txt.gz 2013-09-15 17:34 49K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:53 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:53 482K
chainTarSyr2.sql 2015-05-25 06:34 1.7K
chainTarSyr2.txt.gz 2015-05-25 06:37 3.0G
chainTarSyr2Link.sql 2015-05-25 06:47 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 06:57 7.0G
netTarSyr2.sql 2015-05-25 07:23 2.1K
netTarSyr2.txt.gz 2015-05-25 07:23 64M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.2M
microsat.sql 2015-08-23 23:03 1.5K
microsat.txt.gz 2015-08-23 23:03 84K
all_mrna.sql 2017-07-09 12:08 2.1K
all_mrna.txt.gz 2017-07-09 12:08 261
mrnaOrientInfo.sql 2017-07-09 12:09 1.8K
mrnaOrientInfo.txt.gz 2017-07-09 12:09 137
chainHg38.sql 2018-01-07 09:47 1.7K
chainHg38.txt.gz 2018-01-07 09:47 194M
chainHg38Link.sql 2018-01-07 09:48 1.5K
chainHg38Link.txt.gz 2018-01-07 09:49 867M
netHg38.sql 2018-01-07 09:52 2.1K
netHg38.txt.gz 2018-01-07 09:52 60M
chromAlias.sql 2018-02-18 07:56 1.4K
chromAlias.txt.gz 2018-02-18 07:56 73K
ucscToRefSeq.sql 2018-02-18 07:56 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:56 48K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.5M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 219K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 1.7K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.1M
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.2M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.5M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.9M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 577K
xenoMrna.sql 2020-08-20 00:12 2.1K
xenoMrna.txt.gz 2020-08-20 00:12 448M
xenoRefGene.sql 2020-08-20 00:19 2.0K
xenoRefGene.txt.gz 2020-08-20 00:19 43M
xenoRefFlat.sql 2020-08-20 00:19 1.7K
xenoRefFlat.txt.gz 2020-08-20 00:19 39M
xenoRefSeqAli.sql 2020-08-20 00:19 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 00:19 43M
gbLoaded.sql 2020-08-20 00:19 1.6K
gbLoaded.txt.gz 2020-08-20 00:19 15K
chainMm39.sql 2020-11-24 17:45 1.7K
chainMm39.txt.gz 2020-11-24 17:45 49M
chainMm39Link.sql 2020-11-24 17:48 1.6K
chainMm39Link.txt.gz 2020-11-24 17:48 426M
netMm39.sql 2020-11-24 17:51 2.1K
netMm39.txt.gz 2020-11-24 17:51 59M
ensGene.sql 2021-05-25 14:40 1.9K
ensGene.txt.gz 2021-05-25 14:40 2.1M
ensGtp.sql 2021-05-25 14:40 1.4K
ensGtp.txt.gz 2021-05-25 14:40 278K
ensemblToGeneName.sql 2021-05-25 14:40 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:40 142K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 86K
ensPep.sql 2021-05-25 14:41 1.3K
ensPep.txt.gz 2021-05-25 14:41 6.2M
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 45K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.4K
tableList.sql 2024-11-17 03:37 1.6K
tableList.txt.gz 2024-11-17 03:37 3.3K
bigFiles.sql 2024-11-17 03:37 1.4K
bigFiles.txt.gz 2024-11-17 03:37 94