This directory contains a dump of the UCSC genome annotation database for
the July 2005 (Broad/echTel1) assembly of the tenrec genome (echTel1, Broad July 2005).
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/229058
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=echTel1
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/echTel1/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/echTel1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/echTel1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/echTel1/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 echTel1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql echTel1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
augustusGene.sql 2015-07-26 13:13 1.9K
augustusGene.txt.gz 2015-07-26 13:13 1.7M
bigFiles.sql 2024-11-17 03:34 1.4K
bigFiles.txt.gz 2024-11-17 03:34 68
chainHg19.sql 2012-07-29 11:18 1.7K
chainHg19.txt.gz 2012-07-29 11:19 195M
chainHg19Link.sql 2012-07-29 11:19 1.5K
chainHg19Link.txt.gz 2012-07-29 11:20 646M
chainMm10.sql 2012-06-28 23:14 1.6K
chainMm10.txt.gz 2012-06-28 23:14 67M
chainMm10Link.sql 2012-06-28 23:10 1.5K
chainMm10Link.txt.gz 2012-06-28 23:10 299M
chromAlias.sql 2018-08-05 06:25 1.4K
chromAlias.txt.gz 2018-08-05 06:25 1.4M
chromInfo.sql 2012-06-28 23:09 1.3K
chromInfo.txt.gz 2012-06-28 23:09 1.7M
cpgIslandExt.sql 2012-06-28 23:06 1.6K
cpgIslandExt.txt.gz 2012-06-28 23:06 666K
cpgIslandExtUnmasked.sql 2014-06-01 12:30 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 12:30 641K
cytoBandIdeo.sql 2013-04-28 14:30 1.5K
cytoBandIdeo.txt.gz 2013-04-28 14:30 1.6M
ensGene.sql 2019-02-10 03:41 1.9K
ensGene.txt.gz 2019-02-10 03:41 2.4M
ensGtp.sql 2019-02-10 03:41 1.4K
ensGtp.txt.gz 2019-02-10 03:41 242K
ensPep.sql 2019-02-10 03:41 1.3K
ensPep.txt.gz 2019-02-10 03:41 4.4M
ensemblGeneScaffold.sql 2019-02-10 03:41 1.7K
ensemblGeneScaffold.txt.gz 2019-02-10 03:41 863K
ensemblSource.sql 2019-02-10 03:41 1.4K
ensemblSource.txt.gz 2019-02-10 03:41 74K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensemblToGeneName.txt.gz 2019-02-10 03:41 99K
gap.sql 2012-06-28 23:19 1.7K
gap.txt.gz 2012-06-28 23:19 5.4M
gbLoaded.sql 2020-08-21 15:32 1.6K
gbLoaded.txt.gz 2020-08-21 15:32 14K
gc5BaseBw.sql 2012-06-28 23:09 1.2K
gc5BaseBw.txt.gz 2012-06-28 23:09 63
genscan.sql 2012-06-28 23:19 1.6K
genscan.txt.gz 2012-06-28 23:19 5.1M
genscanSubopt.sql 2012-06-28 23:06 1.5K
genscanSubopt.txt.gz 2012-06-28 23:06 9.3M
gold.sql 2012-06-28 23:09 1.8K
gold.txt.gz 2012-06-28 23:09 11M
grp.sql 2014-03-02 03:40 1.4K
grp.txt.gz 2014-03-02 03:40 223
hgFindSpec.sql 2023-03-28 13:49 1.8K
hgFindSpec.txt.gz 2023-03-28 13:49 669
history.sql 2012-06-28 23:19 1.6K
history.txt.gz 2012-06-28 23:19 1.6K
microsat.sql 2015-08-23 15:42 1.5K
microsat.txt.gz 2015-08-23 15:42 431K
nestedRepeats.sql 2012-06-28 23:07 1.9K
nestedRepeats.txt.gz 2012-06-28 23:07 5.2M
netHg19.sql 2012-07-29 11:23 2.1K
netHg19.txt.gz 2012-07-29 11:23 47M
netMm10.sql 2012-06-28 23:09 2.0K
netMm10.txt.gz 2012-06-28 23:09 27M
quality.sql 2012-06-28 23:07 1.9K
quality.txt.gz 2012-06-28 23:07 73M
rmsk.sql 2012-06-28 23:08 1.8K
rmsk.txt.gz 2012-06-28 23:08 69M
simpleRepeat.sql 2012-06-28 23:06 2.1K
simpleRepeat.txt.gz 2012-06-28 23:06 6.2M
tableDescriptions.sql 2024-11-16 02:03 1.5K
tableDescriptions.txt.gz 2024-11-16 02:03 5.4K
tableList.sql 2024-11-17 03:34 1.6K
tableList.txt.gz 2024-11-17 03:34 2.3K
trackDb.sql 2023-03-28 13:49 2.1K
trackDb.txt.gz 2023-03-28 13:49 20K
windowmaskerSdust.sql 2012-06-28 23:12 1.4K
windowmaskerSdust.txt.gz 2012-06-28 23:12 125M
xenoRefFlat.sql 2020-08-21 15:32 1.7K
xenoRefFlat.txt.gz 2020-08-21 15:32 34M
xenoRefGene.sql 2020-08-21 15:32 2.0K
xenoRefGene.txt.gz 2020-08-21 15:32 38M
xenoRefSeqAli.sql 2020-08-21 15:32 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 15:32 43M