This directory contains a dump of the UCSC genome annotation database for
the Sept. 2008 assembly of the sea hare genome
(aplCal1, Broad Institute v. Aplcal2.0).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the sea hare genome, see the project website:
http://www.broad.mit.edu/node/435
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=aplCal1
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/aplCal1/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/aplCal1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aplCal1/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 aplCal1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql aplCal1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Sea Hare 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 -
bigFiles.txt.gz 2024-11-17 03:16 33
bigFiles.sql 2024-11-17 03:16 1.4K
tableList.txt.gz 2024-11-17 03:16 2.0K
tableList.sql 2024-11-17 03:16 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 4.5K
tableDescriptions.sql 2024-11-16 02:03 1.4K
hgFindSpec.txt.gz 2023-03-28 13:46 545
hgFindSpec.sql 2023-03-28 13:46 1.8K
trackDb.txt.gz 2023-03-28 13:46 20K
trackDb.sql 2023-03-28 13:46 2.1K
gbLoaded.txt.gz 2020-08-18 06:36 28K
gbLoaded.sql 2020-08-18 06:36 1.6K
xenoRefSeqAli.txt.gz 2020-08-18 06:36 11M
xenoRefSeqAli.sql 2020-08-18 06:36 2.1K
xenoRefFlat.txt.gz 2020-08-18 06:17 11M
xenoRefFlat.sql 2020-08-18 06:17 1.7K
xenoRefGene.txt.gz 2020-08-18 06:17 12M
xenoRefGene.sql 2020-08-18 06:17 2.0K
mrnaOrientInfo.txt.gz 2019-03-31 04:11 13K
mrnaOrientInfo.sql 2019-03-31 04:11 1.8K
all_mrna.txt.gz 2019-03-31 04:11 63K
all_mrna.sql 2019-03-31 04:11 2.1K
intronEst.txt.gz 2017-08-06 05:50 3.6M
intronEst.sql 2017-08-06 05:50 2.1K
estOrientInfo.txt.gz 2017-08-06 05:50 3.4M
estOrientInfo.sql 2017-08-06 05:50 1.8K
all_est.txt.gz 2017-08-06 05:50 13M
all_est.sql 2017-08-06 05:50 2.1K
microsat.txt.gz 2015-08-23 09:55 505K
microsat.sql 2015-08-23 09:55 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 08:16 506K
cpgIslandExtUnmasked.sql 2014-06-01 08:16 1.7K
grp.txt.gz 2014-03-02 03:37 208
grp.sql 2014-03-02 03:37 1.4K
chromInfo.txt.gz 2010-03-10 13:26 46K
chromInfo.sql 2010-03-10 13:26 1.3K
rmsk.txt.gz 2010-03-10 13:25 14M
rmsk.sql 2010-03-10 13:25 2.0K
nestedRepeats.txt.gz 2010-03-10 13:25 371K
nestedRepeats.sql 2010-03-10 13:25 2.0K
cpgIslandExt.txt.gz 2010-03-10 13:25 463K
cpgIslandExt.sql 2010-03-10 13:25 1.8K
simpleRepeat.txt.gz 2010-03-10 13:25 16M
simpleRepeat.sql 2010-03-10 13:25 2.0K
quality.txt.gz 2010-03-10 13:25 12M
quality.sql 2010-03-10 13:25 1.9K
gap.txt.gz 2010-03-10 13:24 692K
gap.sql 2010-03-10 13:24 1.6K
gold.txt.gz 2010-03-10 13:24 971K
gold.sql 2010-03-10 13:24 1.7K
blastHg18KG.txt.gz 2010-03-10 13:24 1.4M
blastHg18KG.sql 2010-03-10 13:24 2.3K
gc5Base.txt.gz 2010-03-10 13:24 3.0M
gc5Base.sql 2010-03-10 13:24 1.9K
history.txt.gz 2010-03-10 13:24 418
history.sql 2010-03-10 13:24 1.6K