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:

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:
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

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, 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:// .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file: 
    wget --timestamping 
        -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

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 
   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 - simpleRepeat.txt.gz 2010-03-10 13:25 16M rmsk.txt.gz 2010-03-10 13:25 14M all_est.txt.gz 2017-08-06 05:50 13M xenoRefGene.txt.gz 2020-08-18 06:17 12M quality.txt.gz 2010-03-10 13:25 12M xenoRefSeqAli.txt.gz 2020-08-18 06:36 11M xenoRefFlat.txt.gz 2020-08-18 06:17 11M intronEst.txt.gz 2017-08-06 05:50 3.6M estOrientInfo.txt.gz 2017-08-06 05:50 3.4M gc5Base.txt.gz 2010-03-10 13:24 3.0M blastHg18KG.txt.gz 2010-03-10 13:24 1.4M gold.txt.gz 2010-03-10 13:24 971K gap.txt.gz 2010-03-10 13:24 692K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:16 506K microsat.txt.gz 2015-08-23 09:55 505K cpgIslandExt.txt.gz 2010-03-10 13:25 463K nestedRepeats.txt.gz 2010-03-10 13:25 371K all_mrna.txt.gz 2019-03-31 04:11 63K chromInfo.txt.gz 2010-03-10 13:26 46K gbLoaded.txt.gz 2020-08-18 06:36 28K trackDb.txt.gz 2023-03-28 13:46 20K mrnaOrientInfo.txt.gz 2019-03-31 04:11 13K tableDescriptions.txt.gz 2024-06-15 02:03 4.5K blastHg18KG.sql 2010-03-10 13:24 2.3K xenoRefSeqAli.sql 2020-08-18 06:36 2.1K intronEst.sql 2017-08-06 05:50 2.1K all_mrna.sql 2019-03-31 04:11 2.1K all_est.sql 2017-08-06 05:50 2.1K trackDb.sql 2023-03-28 13:46 2.1K tableList.txt.gz 2024-06-16 03:07 2.0K simpleRepeat.sql 2010-03-10 13:25 2.0K nestedRepeats.sql 2010-03-10 13:25 2.0K rmsk.sql 2010-03-10 13:25 2.0K xenoRefGene.sql 2020-08-18 06:17 2.0K quality.sql 2010-03-10 13:25 1.9K gc5Base.sql 2010-03-10 13:24 1.9K mrnaOrientInfo.sql 2019-03-31 04:11 1.8K estOrientInfo.sql 2017-08-06 05:50 1.8K hgFindSpec.sql 2023-03-28 13:46 1.8K cpgIslandExt.sql 2010-03-10 13:25 1.8K xenoRefFlat.sql 2020-08-18 06:17 1.7K cpgIslandExtUnmasked.sql 2014-06-01 08:16 1.7K gold.sql 2010-03-10 13:24 1.7K gap.sql 2010-03-10 13:24 1.6K gbLoaded.sql 2020-08-18 06:36 1.6K tableList.sql 2024-06-16 03:07 1.6K history.sql 2010-03-10 13:24 1.6K microsat.sql 2015-08-23 09:55 1.5K tableDescriptions.sql 2024-06-15 02:03 1.4K grp.sql 2014-03-02 03:37 1.4K bigFiles.sql 2024-06-16 03:07 1.4K chromInfo.sql 2010-03-10 13:26 1.3K hgFindSpec.txt.gz 2023-03-28 13:46 545 history.txt.gz 2010-03-10 13:24 418 grp.txt.gz 2014-03-02 03:37 208 bigFiles.txt.gz 2024-06-16 03:07 33