This directory contains a dump of the UCSC genome annotation database for the
Nov. 2012 (Broad/echTel2) assembly of the tenrec genome
(echTel2, Broad/EchTel2.0) .
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/234
http://www.ncbi.nlm.nih.gov/genome/assembly/500848
http://www.ncbi.nlm.nih.gov/bioproject/12590
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=echTel2
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/echTel2/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/echTel2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/echTel2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel2/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 echTel2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql echTel2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Tenrec 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 -
augustusGene.sql 26-Jul-2015 13:14 1.9K
augustusGene.txt.gz 26-Jul-2015 13:14 2.6M
bigFiles.sql 23-Jul-2017 04:09 1.4K
bigFiles.txt.gz 23-Jul-2017 04:09 68
chainHg19.sql 29-Aug-2013 12:41 1.7K
chainHg19.txt.gz 29-Aug-2013 12:41 227M
chainHg19Link.sql 29-Aug-2013 12:34 1.5K
chainHg19Link.txt.gz 29-Aug-2013 12:37 813M
chainMm10.sql 29-Aug-2013 12:43 1.7K
chainMm10.txt.gz 29-Aug-2013 12:43 65M
chainMm10Link.sql 29-Aug-2013 12:32 1.5K
chainMm10Link.txt.gz 29-Aug-2013 12:32 367M
chromInfo.sql 29-Aug-2013 12:41 1.4K
chromInfo.txt.gz 29-Aug-2013 12:41 38K
cpgIslandExt.sql 29-Aug-2013 12:41 1.7K
cpgIslandExt.txt.gz 29-Aug-2013 12:41 757K
cpgIslandExtUnmasked.sql 01-Jun-2014 12:32 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 12:32 840K
cytoBandIdeo.sql 29-Aug-2013 12:34 1.5K
cytoBandIdeo.txt.gz 29-Aug-2013 12:34 38K
gap.sql 29-Aug-2013 12:34 1.6K
gap.txt.gz 29-Aug-2013 12:34 3.7M
gbLoaded.sql 09-Jul-2017 08:56 1.6K
gbLoaded.txt.gz 09-Jul-2017 08:56 2.9K
gc5BaseBw.sql 29-Aug-2013 12:43 1.3K
gc5BaseBw.txt.gz 29-Aug-2013 12:43 63
genscan.sql 29-Aug-2013 12:32 1.7K
genscan.txt.gz 29-Aug-2013 12:32 4.3M
genscanSubopt.sql 29-Aug-2013 12:43 1.6K
genscanSubopt.txt.gz 29-Aug-2013 12:43 7.5M
gold.sql 29-Aug-2013 12:32 1.7K
gold.txt.gz 29-Aug-2013 12:32 4.6M
grp.sql 02-Mar-2014 03:40 1.3K
grp.txt.gz 02-Mar-2014 03:40 208
hgFindSpec.sql 23-Jul-2017 04:09 1.7K
hgFindSpec.txt.gz 23-Jul-2017 04:09 369
history.sql 29-Aug-2013 12:34 1.6K
history.txt.gz 29-Aug-2013 12:34 461
microsat.sql 23-Aug-2015 15:43 1.5K
microsat.txt.gz 23-Aug-2015 15:43 533K
nestedRepeats.sql 29-Aug-2013 12:42 1.9K
nestedRepeats.txt.gz 29-Aug-2013 12:42 8.7M
netHg19.sql 29-Aug-2013 12:34 2.1K
netHg19.txt.gz 29-Aug-2013 12:34 54M
netMm10.sql 29-Aug-2013 12:40 2.1K
netMm10.txt.gz 29-Aug-2013 12:40 31M
rmsk.sql 29-Aug-2013 12:43 1.9K
rmsk.txt.gz 29-Aug-2013 12:43 94M
simpleRepeat.sql 29-Aug-2013 12:42 1.9K
simpleRepeat.txt.gz 29-Aug-2013 12:42 11M
tableDescriptions.sql 23-Jul-2017 04:09 1.4K
tableDescriptions.txt.gz 23-Jul-2017 04:09 3.7K
tableList.sql 23-Jul-2017 04:09 1.5K
tableList.txt.gz 23-Jul-2017 04:09 2.0K
trackDb.sql 23-Jul-2017 04:09 2.0K
trackDb.txt.gz 23-Jul-2017 04:09 23K
windowmaskerSdust.sql 29-Aug-2013 12:42 1.5K
windowmaskerSdust.txt.gz 29-Aug-2013 12:42 156M
xenoRefFlat.sql 09-Jul-2017 08:56 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 08:56 29M
xenoRefGene.sql 09-Jul-2017 08:56 1.9K
xenoRefGene.txt.gz 09-Jul-2017 08:56 33M
xenoRefSeqAli.sql 09-Jul-2017 08:56 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 08:56 28M