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 - xenoRefSeqAli.txt.gz 2020-08-18 11:45 24M xenoRefSeqAli.sql 2020-08-18 11:45 2.1K xenoRefGene.txt.gz 2020-08-18 11:37 27M xenoRefGene.sql 2020-08-18 11:37 2.0K xenoRefFlat.txt.gz 2020-08-18 11:40 24M xenoRefFlat.sql 2020-08-18 11:40 1.7K windowmaskerSdust.txt.gz 2014-05-08 14:04 50M windowmaskerSdust.sql 2014-05-08 14:04 1.5K ucscToRefSeq.txt.gz 2018-02-18 05:32 125K ucscToRefSeq.sql 2018-02-18 05:32 1.4K ucscToINSDC.txt.gz 2014-05-08 14:04 122K ucscToINSDC.sql 2014-05-08 14:04 1.4K trackDb_pushedout.txt.gz 2023-12-05 13:52 31K trackDb_pushedout.sql 2023-12-05 13:52 2.1K trackDb.txt.gz 2023-12-05 13:52 31K trackDb.sql 2023-12-05 13:52 2.1K tableList.txt.gz 2024-04-21 03:29 3.1K tableList.sql 2024-04-21 03:29 1.6K tableDescriptions.txt.gz 2024-04-20 02:03 6.3K tableDescriptions.sql 2024-04-20 02:03 1.4K simpleRepeat.txt.gz 2014-05-08 14:04 8.6M simpleRepeat.sql 2014-05-08 14:04 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 458K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K rmsk.txt.gz 2014-05-08 14:04 36M rmsk.sql 2014-05-08 14:04 1.9K netRn6.txt.gz 2017-03-26 15:43 5.6M netRn6.sql 2017-03-26 15:43 2.1K nestedRepeats.txt.gz 2014-05-08 14:03 2.0M nestedRepeats.sql 2014-05-08 14:03 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 2.5M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 6.0M ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 895K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 325 ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 185K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:26 2.1M ncbiRefSeq.sql 2020-05-10 03:26 1.9K mrnaOrientInfo.txt.gz 2017-04-09 11:47 485K mrnaOrientInfo.sql 2017-04-09 11:47 1.8K microsat.txt.gz 2015-08-23 11:24 33K microsat.sql 2015-08-23 11:24 1.5K intronEst.txt.gz 2016-05-15 07:51 2.0M intronEst.sql 2016-05-15 07:51 2.1K history.txt.gz 2014-05-08 14:03 402 history.sql 2014-05-08 14:03 1.6K hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.2K hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K hgFindSpec.txt.gz 2023-12-05 13:52 1.2K hgFindSpec.sql 2023-12-05 13:52 1.8K grp.txt.gz 2014-08-03 06:48 200 grp.sql 2014-08-03 06:48 1.3K gold.txt.gz 2014-05-08 14:03 898K gold.sql 2014-05-08 14:03 1.7K genscanSubopt.txt.gz 2014-05-08 14:03 2.8M genscanSubopt.sql 2014-05-08 14:03 1.6K genscan.txt.gz 2014-05-08 14:03 1.9M genscan.sql 2014-05-08 14:03 1.7K gc5BaseBw.txt.gz 2014-05-08 14:04 66 gc5BaseBw.sql 2014-05-08 14:04 1.3K gbLoaded.txt.gz 2020-08-18 11:45 44K gbLoaded.sql 2020-08-18 11:45 1.6K gap.txt.gz 2014-05-08 14:03 571K gap.sql 2014-05-08 14:03 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:26 90 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K estOrientInfo.txt.gz 2016-05-15 07:51 1.2M estOrientInfo.sql 2016-05-15 07:51 1.8K ensemblToGeneName.txt.gz 2021-05-25 14:22 167K ensemblToGeneName.sql 2021-05-25 14:22 1.4K ensemblSource.txt.gz 2021-05-25 14:24 124K ensemblSource.sql 2021-05-25 14:24 1.4K ensPep.txt.gz 2021-05-25 14:24 7.0M ensPep.sql 2021-05-25 14:24 1.3K ensGtp.txt.gz 2021-05-25 14:22 412K ensGtp.sql 2021-05-25 14:22 1.4K ensGene.txt.gz 2021-05-25 14:22 2.8M ensGene.sql 2021-05-25 14:22 1.9K cytoBandIdeo.txt.gz 2014-05-08 14:03 71K cytoBandIdeo.sql 2014-05-08 14:03 1.5K cpgIslandExtUnmasked.txt.gz 2014-05-08 14:03 710K cpgIslandExtUnmasked.sql 2014-05-08 14:03 1.7K cpgIslandExt.txt.gz 2014-05-08 14:03 376K cpgIslandExt.sql 2014-05-08 14:03 1.7K chromInfo.txt.gz 2014-05-08 14:03 74K chromInfo.sql 2014-05-08 14:03 1.4K chromAlias.txt.gz 2020-04-12 03:25 206K chromAlias.sql 2020-04-12 03:25 1.4K chainRn6Link.txt.gz 2017-03-26 15:24 312M chainRn6Link.sql 2017-03-26 15:21 1.5K chainRn6.txt.gz 2017-03-26 15:19 78M chainRn6.sql 2017-03-26 15:18 1.7K bigFiles.txt.gz 2024-04-21 03:29 95 bigFiles.sql 2024-04-21 03:29 1.4K augustusGene.txt.gz 2015-07-26 10:55 1.7M augustusGene.sql 2015-07-26 10:55 1.9K all_mrna.txt.gz 2017-04-09 11:50 2.2M all_mrna.sql 2017-04-09 11:50 2.1K all_est.txt.gz 2016-05-15 07:51 3.9M all_est.sql 2016-05-15 07:51 2.1K