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.

---------------------------------------------------------------
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 - all_est.sql 2017-08-06 05:50 2.1K all_est.txt.gz 2017-08-06 05:50 13M all_mrna.sql 2019-03-31 04:11 2.1K all_mrna.txt.gz 2019-03-31 04:11 63K bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 33 blastHg18KG.sql 2010-03-10 13:24 2.3K blastHg18KG.txt.gz 2010-03-10 13:24 1.4M chromInfo.sql 2010-03-10 13:26 1.3K chromInfo.txt.gz 2010-03-10 13:26 46K cpgIslandExt.sql 2010-03-10 13:25 1.8K cpgIslandExt.txt.gz 2010-03-10 13:25 463K cpgIslandExtUnmasked.sql 2014-06-01 08:16 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:16 506K estOrientInfo.sql 2017-08-06 05:50 1.8K estOrientInfo.txt.gz 2017-08-06 05:50 3.4M gap.sql 2010-03-10 13:24 1.6K gap.txt.gz 2010-03-10 13:24 692K gbLoaded.sql 2020-08-18 06:36 1.6K gbLoaded.txt.gz 2020-08-18 06:36 28K gc5Base.sql 2010-03-10 13:24 1.9K gc5Base.txt.gz 2010-03-10 13:24 3.0M gold.sql 2010-03-10 13:24 1.7K gold.txt.gz 2010-03-10 13:24 971K grp.sql 2014-03-02 03:37 1.4K grp.txt.gz 2014-03-02 03:37 208 hgFindSpec.sql 2020-12-06 07:38 1.7K hgFindSpec.txt.gz 2020-12-06 07:38 495 history.sql 2010-03-10 13:24 1.6K history.txt.gz 2010-03-10 13:24 418 intronEst.sql 2017-08-06 05:50 2.1K intronEst.txt.gz 2017-08-06 05:50 3.6M microsat.sql 2015-08-23 09:55 1.5K microsat.txt.gz 2015-08-23 09:55 505K mrnaOrientInfo.sql 2019-03-31 04:11 1.8K mrnaOrientInfo.txt.gz 2019-03-31 04:11 13K nestedRepeats.sql 2010-03-10 13:25 2.0K nestedRepeats.txt.gz 2010-03-10 13:25 371K quality.sql 2010-03-10 13:25 1.9K quality.txt.gz 2010-03-10 13:25 12M rmsk.sql 2010-03-10 13:25 2.0K rmsk.txt.gz 2010-03-10 13:25 14M simpleRepeat.sql 2010-03-10 13:25 2.0K simpleRepeat.txt.gz 2010-03-10 13:25 16M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 4.5K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 2.0K trackDb.sql 2020-12-06 07:38 2.0K trackDb.txt.gz 2020-12-06 07:38 16K xenoRefFlat.sql 2020-08-18 06:17 1.7K xenoRefFlat.txt.gz 2020-08-18 06:17 11M xenoRefGene.sql 2020-08-18 06:17 1.9K xenoRefGene.txt.gz 2020-08-18 06:17 12M xenoRefSeqAli.sql 2020-08-18 06:36 2.1K xenoRefSeqAli.txt.gz 2020-08-18 06:36 11M