This directory contains a dump of the UCSC genome annotation database for the
    Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1) assembly of the elephant shark genome
    (calMil1, Institute of Molecular and Cell Biology, Singapore) .

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/689
    http://www.ncbi.nlm.nih.gov/genome/assembly/85971
    http://www.ncbi.nlm.nih.gov/bioproject/18361

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=calMil1
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/calMil1/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/calMil1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/calMil1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/calMil1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/calMil1/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 calMil1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calMil1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - all_est.sql 2016-05-15 07:51 2.1K all_est.txt.gz 2016-05-15 07:51 3.9M all_mrna.sql 2017-04-09 11:50 2.1K all_mrna.txt.gz 2017-04-09 11:50 2.2M augustusGene.sql 2015-07-26 10:55 1.9K augustusGene.txt.gz 2015-07-26 10:55 1.7M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 95 chainRn6.sql 2017-03-26 15:18 1.7K chainRn6.txt.gz 2017-03-26 15:19 78M chainRn6Link.sql 2017-03-26 15:21 1.5K chainRn6Link.txt.gz 2017-03-26 15:24 312M chromAlias.sql 2020-04-12 03:25 1.4K chromAlias.txt.gz 2020-04-12 03:25 206K chromInfo.sql 2014-05-08 14:03 1.4K chromInfo.txt.gz 2014-05-08 14:03 74K cpgIslandExt.sql 2014-05-08 14:03 1.7K cpgIslandExt.txt.gz 2014-05-08 14:03 376K cpgIslandExtUnmasked.sql 2014-05-08 14:03 1.7K cpgIslandExtUnmasked.txt.gz 2014-05-08 14:03 710K cytoBandIdeo.sql 2014-05-08 14:03 1.5K cytoBandIdeo.txt.gz 2014-05-08 14:03 71K ensGene.sql 2020-08-31 15:19 1.9K ensGene.txt.gz 2020-08-31 15:19 2.8M ensGtp.sql 2020-08-31 15:19 1.4K ensGtp.txt.gz 2020-08-31 15:19 411K ensPep.sql 2020-08-31 15:42 1.3K ensPep.txt.gz 2020-08-31 15:42 7.0M ensemblSource.sql 2020-08-31 15:42 1.4K ensemblSource.txt.gz 2020-08-31 15:42 124K ensemblToGeneName.sql 2020-08-31 15:19 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:19 164K estOrientInfo.sql 2016-05-15 07:51 1.8K estOrientInfo.txt.gz 2016-05-15 07:51 1.2M extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 90 gap.sql 2014-05-08 14:03 1.6K gap.txt.gz 2014-05-08 14:03 571K gbLoaded.sql 2020-08-18 11:45 1.6K gbLoaded.txt.gz 2020-08-18 11:45 44K gc5BaseBw.sql 2014-05-08 14:04 1.3K gc5BaseBw.txt.gz 2014-05-08 14:04 66 genscan.sql 2014-05-08 14:03 1.7K genscan.txt.gz 2014-05-08 14:03 1.9M genscanSubopt.sql 2014-05-08 14:03 1.6K genscanSubopt.txt.gz 2014-05-08 14:03 2.8M gold.sql 2014-05-08 14:03 1.7K gold.txt.gz 2014-05-08 14:03 898K grp.sql 2014-08-03 06:48 1.3K grp.txt.gz 2014-08-03 06:48 200 hgFindSpec.sql 2020-12-06 07:44 1.7K hgFindSpec.txt.gz 2020-12-06 07:44 1.1K history.sql 2014-05-08 14:03 1.6K history.txt.gz 2014-05-08 14:03 402 intronEst.sql 2016-05-15 07:51 2.1K intronEst.txt.gz 2016-05-15 07:51 2.0M microsat.sql 2015-08-23 11:24 1.5K microsat.txt.gz 2015-08-23 11:24 33K mrnaOrientInfo.sql 2017-04-09 11:47 1.8K mrnaOrientInfo.txt.gz 2017-04-09 11:47 485K ncbiRefSeq.sql 2020-05-10 03:26 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 185K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 325 ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 895K ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 6.0M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 2.5M nestedRepeats.sql 2014-05-08 14:03 1.9K nestedRepeats.txt.gz 2014-05-08 14:03 2.0M netRn6.sql 2017-03-26 15:43 2.1K netRn6.txt.gz 2017-03-26 15:43 5.6M rmsk.sql 2014-05-08 14:04 1.9K rmsk.txt.gz 2014-05-08 14:04 36M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 458K simpleRepeat.sql 2014-05-08 14:04 1.9K simpleRepeat.txt.gz 2014-05-08 14:04 8.6M tableDescriptions.sql 2020-04-26 03:23 1.4K tableDescriptions.txt.gz 2020-04-26 03:23 6.3K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 2.9K trackDb.sql 2020-12-06 07:44 2.0K trackDb.txt.gz 2020-12-06 07:44 42K ucscToINSDC.sql 2014-05-08 14:04 1.4K ucscToINSDC.txt.gz 2014-05-08 14:04 122K ucscToRefSeq.sql 2018-02-18 05:32 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:32 125K windowmaskerSdust.sql 2014-05-08 14:04 1.5K windowmaskerSdust.txt.gz 2014-05-08 14:04 50M xenoRefFlat.sql 2020-08-18 11:40 1.7K xenoRefFlat.txt.gz 2020-08-18 11:40 24M xenoRefGene.sql 2020-08-18 11:37 1.9K xenoRefGene.txt.gz 2020-08-18 11:37 27M xenoRefSeqAli.sql 2020-08-18 11:45 2.1K xenoRefSeqAli.txt.gz 2020-08-18 11:45 24M