This directory contains a dump of the UCSC genome annotation database for
the Dec. 2006 (Broad/tupBel1) assembly of the tree shrew genome (tupBel1, Broad Institute tupBel1 (NCBI project 13971, AAPY01000000)).
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/473
http://www.ncbi.nlm.nih.gov/genome/assembly/229078
http://www.ncbi.nlm.nih.gov/bioproject/13971
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=tupBel1
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/tupBel1/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/tupBel1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/tupBel1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tupBel1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tupBel1/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 tupBel1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql tupBel1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Tree shrew 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.
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Name Last modified Size Description
Parent Directory -
all_est.sql 2012-11-16 12:51 2.1K
all_est.txt.gz 2012-11-16 12:51 334K
all_mrna.sql 2017-12-03 08:59 2.1K
all_mrna.txt.gz 2017-12-03 08:59 14K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.0M
bigFiles.sql 2024-11-17 03:22 1.4K
bigFiles.txt.gz 2024-11-17 03:22 33
chainGalVar1.sql 2016-09-18 11:27 1.7K
chainGalVar1.txt.gz 2016-09-18 11:28 1.2G
chainGalVar1Link.sql 2016-09-18 11:32 1.5K
chainGalVar1Link.txt.gz 2016-09-18 11:36 3.2G
chainMm10.sql 2012-11-16 12:55 1.7K
chainMm10.txt.gz 2012-11-16 12:55 113M
chainMm10Link.sql 2012-11-16 12:51 1.5K
chainMm10Link.txt.gz 2012-11-16 12:52 544M
chainMm39.sql 2020-11-26 06:45 1.7K
chainMm39.txt.gz 2020-11-26 06:45 100M
chainMm39Link.sql 2020-11-26 06:49 1.6K
chainMm39Link.txt.gz 2020-11-26 06:49 504M
chainTarSyr2.sql 2015-05-25 13:27 1.7K
chainTarSyr2.txt.gz 2015-05-25 13:28 433M
chainTarSyr2Link.sql 2015-05-25 13:29 1.5K
chainTarSyr2Link.txt.gz 2015-05-25 13:31 1.3G
chromAlias.sql 2018-08-05 09:37 1.4K
chromAlias.txt.gz 2018-08-05 09:37 1.0M
chromInfo.sql 2012-11-16 12:54 1.4K
chromInfo.txt.gz 2012-11-16 12:54 1.1M
cpgIslandExt.sql 2012-11-16 12:51 1.7K
cpgIslandExt.txt.gz 2012-11-16 12:51 1.2M
cpgIslandExtUnmasked.sql 2014-06-01 20:15 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:15 1.2M
cytoBandIdeo.sql 2013-04-28 22:39 1.5K
cytoBandIdeo.txt.gz 2013-04-28 22:39 1.1M
ensGene.sql 2019-02-10 03:42 1.9K
ensGene.txt.gz 2019-02-10 03:42 2.0M
ensGtp.sql 2019-02-10 03:42 1.4K
ensGtp.txt.gz 2019-02-10 03:42 200K
ensPep.sql 2019-02-10 03:42 1.3K
ensPep.txt.gz 2019-02-10 03:42 4.1M
ensemblGeneScaffold.sql 2019-02-10 03:42 1.7K
ensemblGeneScaffold.txt.gz 2019-02-10 03:42 843K
ensemblSource.sql 2019-02-10 03:42 1.4K
ensemblSource.txt.gz 2019-02-10 03:42 58K
ensemblToGeneName.sql 2019-02-10 03:42 1.4K
ensemblToGeneName.txt.gz 2019-02-10 03:42 88K
estOrientInfo.sql 2012-11-16 12:56 1.8K
estOrientInfo.txt.gz 2012-11-16 12:56 144K
gap.sql 2012-11-16 12:56 1.7K
gap.txt.gz 2012-11-16 12:56 9.6M
gbLoaded.sql 2020-08-20 16:37 1.6K
gbLoaded.txt.gz 2020-08-20 16:37 87K
gc5Base.sql 2012-11-16 12:54 1.9K
gc5Base.txt.gz 2012-11-16 12:54 16M
genscan.sql 2012-11-16 12:54 1.7K
genscan.txt.gz 2012-11-16 12:54 3.9M
gold.sql 2012-11-16 12:49 1.8K
gold.txt.gz 2012-11-16 12:49 15M
grp.sql 2014-03-02 04:18 1.4K
grp.txt.gz 2014-03-02 04:18 208
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 753
history.sql 2012-11-16 12:54 1.6K
history.txt.gz 2012-11-16 12:54 1.1K
intronEst.sql 2012-11-16 12:50 2.1K
intronEst.txt.gz 2012-11-16 12:50 13K
microsat.sql 2015-08-24 02:50 1.5K
microsat.txt.gz 2015-08-24 02:50 867K
mrnaOrientInfo.sql 2017-12-03 08:59 1.8K
mrnaOrientInfo.txt.gz 2017-12-03 08:59 4.3K
nestedRepeats.sql 2012-11-16 12:56 2.1K
nestedRepeats.txt.gz 2012-11-16 12:56 6.6M
netGalVar1.sql 2016-09-18 11:49 2.1K
netGalVar1.txt.gz 2016-09-18 11:49 70M
netMm10.sql 2012-11-16 12:54 2.1K
netMm10.txt.gz 2012-11-16 12:54 48M
netMm39.sql 2020-11-26 06:52 2.1K
netMm39.txt.gz 2020-11-26 06:52 48M
netTarSyr2.sql 2015-05-25 13:36 2.1K
netTarSyr2.txt.gz 2015-05-25 13:36 65M
quality.sql 2012-11-16 12:49 1.9K
quality.txt.gz 2012-11-16 12:49 74M
rmsk.sql 2012-11-16 12:55 2.1K
rmsk.txt.gz 2012-11-16 12:55 78M
simpleRepeat.sql 2012-11-16 12:51 2.1K
simpleRepeat.txt.gz 2012-11-16 12:51 19M
tableDescriptions.sql 2024-11-16 02:04 1.4K
tableDescriptions.txt.gz 2024-11-16 02:04 5.7K
tableList.sql 2024-11-17 03:22 1.6K
tableList.txt.gz 2024-11-17 03:22 3.0K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 43K
windowmaskerSdust.sql 2012-11-16 12:49 1.5K
windowmaskerSdust.txt.gz 2012-11-16 12:49 117M
xenoRefFlat.sql 2020-08-20 16:37 1.7K
xenoRefFlat.txt.gz 2020-08-20 16:37 43M
xenoRefGene.sql 2020-08-20 16:37 2.0K
xenoRefGene.txt.gz 2020-08-20 16:37 47M
xenoRefSeqAli.sql 2020-08-20 16:37 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 16:37 50M