This directory contains a dump of the UCSC genome annotation database for the
Oct. 2011 (Baylor Ttru_1.4/turTru2) assembly of the dolphin genome (turTru2,
Baylor College of Medicine Ttru_1.4 (NCBI project 20365, GCA_000151865.2, WGS ABRN02)).
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/769
    http://www.ncbi.nlm.nih.gov/genome/assembly/325108
    http://www.ncbi.nlm.nih.gov/bioproject/20367

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=turTru2
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/turTru2/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/turTru2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/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 turTru2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql turTru2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

For conditions of use regarding the Dolphin genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use

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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.

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All the files and tables in this directory are freely usable for any purpose.
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      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2019-01-03 14:01 63 bigFiles.txt.gz 2022-08-07 03:10 68 grp.txt.gz 2019-01-03 14:01 208 hgFindSpec.txt.gz 2021-08-02 14:33 530 history.txt.gz 2019-01-03 14:01 561 gc5BaseBw.sql 2019-01-03 14:01 1.3K grp.sql 2019-01-03 14:01 1.3K bigFiles.sql 2022-08-07 03:10 1.4K chromInfo.sql 2019-01-03 14:01 1.4K tableDescriptions.sql 2021-03-13 06:37 1.4K ucscToINSDC.sql 2019-01-03 14:02 1.4K microsat.sql 2019-01-03 14:01 1.5K windowmaskerSdust.sql 2019-01-03 14:02 1.5K cytoBandIdeo.sql 2019-01-03 14:01 1.5K chainMm10Link.sql 2019-01-03 13:59 1.5K chainBosTau7Link.sql 2019-01-03 13:36 1.5K chainMm39Link.sql 2020-11-24 20:21 1.6K tableList.sql 2022-08-07 03:10 1.6K history.sql 2019-01-03 14:01 1.6K gbLoaded.sql 2020-08-20 17:43 1.6K gap.sql 2019-01-03 14:01 1.6K gold.sql 2019-01-03 14:01 1.7K genscan.sql 2019-01-03 14:01 1.7K cpgIslandExt.sql 2019-01-03 14:01 1.7K chainMm10.sql 2019-01-03 13:59 1.7K chainBosTau7.sql 2019-01-03 13:30 1.7K cpgIslandExtUnmasked.sql 2019-01-03 14:01 1.7K xenoRefFlat.sql 2020-08-20 17:29 1.7K chainMm39.sql 2020-11-24 20:19 1.7K hgFindSpec.sql 2021-08-02 14:33 1.8K rmsk.sql 2019-01-03 14:01 1.9K simpleRepeat.sql 2019-01-03 14:02 1.9K nestedRepeats.sql 2019-01-03 14:01 1.9K xenoRefGene.sql 2020-08-20 17:29 1.9K augustusGene.sql 2019-01-03 13:30 1.9K trackDb.sql 2021-08-02 14:33 2.1K netMm10.sql 2019-01-03 14:01 2.1K netBosTau7.sql 2019-01-03 14:01 2.1K tableList.txt.gz 2022-08-07 03:10 2.1K netMm39.sql 2020-11-24 20:24 2.1K xenoRefSeqAli.sql 2020-08-20 17:29 2.1K tableDescriptions.txt.gz 2021-03-13 06:37 4.8K gbLoaded.txt.gz 2020-08-20 17:43 14K trackDb.txt.gz 2021-08-02 14:33 32K microsat.txt.gz 2019-01-03 14:01 458K cpgIslandExt.txt.gz 2019-01-03 14:01 966K cytoBandIdeo.txt.gz 2019-01-03 14:01 1.0M chromInfo.txt.gz 2019-01-03 14:01 1.0M cpgIslandExtUnmasked.txt.gz 2019-01-03 14:01 1.4M ucscToINSDC.txt.gz 2019-01-03 14:02 1.6M augustusGene.txt.gz 2019-01-03 13:30 2.1M genscan.txt.gz 2019-01-03 14:01 2.9M gap.txt.gz 2019-01-03 14:01 3.5M gold.txt.gz 2019-01-03 14:01 6.6M nestedRepeats.txt.gz 2019-01-03 14:01 11M simpleRepeat.txt.gz 2019-01-03 14:02 16M chainMm39.txt.gz 2020-11-24 20:19 21M chainMm10.txt.gz 2019-01-03 13:59 33M xenoRefFlat.txt.gz 2020-08-20 17:29 34M xenoRefGene.txt.gz 2020-08-20 17:29 38M xenoRefSeqAli.txt.gz 2020-08-20 17:29 42M netBosTau7.txt.gz 2019-01-03 14:01 61M netMm39.txt.gz 2020-11-24 20:24 61M netMm10.txt.gz 2019-01-03 14:01 61M rmsk.txt.gz 2019-01-03 14:01 106M windowmaskerSdust.txt.gz 2019-01-03 14:02 121M chainMm39Link.txt.gz 2020-11-24 20:21 291M chainMm10Link.txt.gz 2019-01-03 13:59 326M chainBosTau7.txt.gz 2019-01-03 13:31 1.5G chainBosTau7Link.txt.gz 2019-01-03 13:42 4.4G