This directory contains a dump of the UCSC genome annotation database for the
    Dec. 2009 (UMD_3.1.1/bosTau8) assembly of the cow genome
    (bosTau8, University of Maryland Bos_taurus_UMD_3.1.1) .

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/82
    http://www.ncbi.nlm.nih.gov/genome/assembly/189361
    http://www.ncbi.nlm.nih.gov/bioproject/33843

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=bosTau8
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/bosTau8/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/bosTau8/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau8/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 bosTau8 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau8 --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 2015-03-02 10:39 2.1K all_est.txt.gz 2015-03-02 10:39 61M all_mrna.sql 2020-08-20 21:06 2.1K all_mrna.txt.gz 2020-08-20 21:06 1.6M augustusGene.sql 2015-07-26 10:22 1.9K augustusGene.txt.gz 2015-07-26 10:22 2.3M bigFiles.sql 2022-06-19 03:06 1.4K bigFiles.txt.gz 2022-06-19 03:06 69 chainEquCab2.sql 2015-02-24 10:54 1.7K chainEquCab2.txt.gz 2015-02-24 10:54 241M chainEquCab2Link.sql 2015-02-24 10:56 1.5K chainEquCab2Link.txt.gz 2015-02-24 10:57 1.2G chainHg38.sql 2014-12-17 12:23 1.7K chainHg38.txt.gz 2014-12-17 12:23 237M chainHg38Link.sql 2014-12-17 12:24 1.5K chainHg38Link.txt.gz 2014-12-17 12:25 1.0G chainMm10.sql 2014-12-17 12:29 1.7K chainMm10.txt.gz 2014-12-17 12:29 65M chainMm10Link.sql 2014-12-17 12:29 1.5K chainMm10Link.txt.gz 2014-12-17 12:30 494M chainRn6.sql 2017-03-26 13:25 1.7K chainRn6.txt.gz 2017-03-26 13:25 114M chainRn6Link.sql 2017-03-26 13:33 1.5K chainRn6Link.txt.gz 2017-03-26 13:45 653M chromAlias.sql 2018-02-18 05:20 1.4K chromAlias.txt.gz 2018-02-18 05:20 32K chromInfo.sql 2014-12-17 12:32 1.4K chromInfo.txt.gz 2014-12-17 12:32 17K cpgIslandExt.sql 2014-12-17 12:32 1.7K cpgIslandExt.txt.gz 2014-12-17 12:32 803K cpgIslandExtUnmasked.sql 2014-12-17 12:32 1.7K cpgIslandExtUnmasked.txt.gz 2014-12-17 12:32 922K cytoBandIdeo.sql 2014-12-17 12:32 1.5K cytoBandIdeo.txt.gz 2014-12-17 12:32 17K estOrientInfo.sql 2015-03-02 10:40 1.8K estOrientInfo.txt.gz 2015-03-02 10:40 19M gap.sql 2014-12-17 12:32 1.6K gap.txt.gz 2014-12-17 12:32 948K gbLoaded.sql 2020-08-20 21:06 1.6K gbLoaded.txt.gz 2020-08-20 21:06 60K gc5BaseBw.sql 2014-12-17 12:32 1.3K gc5BaseBw.txt.gz 2014-12-17 12:32 66 geneid.sql 2015-11-22 13:03 1.9K geneid.txt.gz 2015-11-22 13:03 2.2M genscan.sql 2014-12-17 12:32 1.7K genscan.txt.gz 2014-12-17 12:32 3.0M genscanSubopt.sql 2014-12-17 12:32 1.6K genscanSubopt.txt.gz 2014-12-17 12:32 5.5M gold.sql 2014-12-17 12:32 1.7K gold.txt.gz 2014-12-17 12:32 1.3M grp.sql 2014-12-17 12:32 1.3K grp.txt.gz 2014-12-17 12:32 205 hgFindSpec.sql 2021-12-17 16:15 1.8K hgFindSpec.txt.gz 2021-12-17 16:15 815 history.sql 2014-12-17 12:23 1.6K history.txt.gz 2014-12-17 12:23 537 intronEst.sql 2015-03-02 10:39 2.1K intronEst.txt.gz 2015-03-02 10:39 37M microsat.sql 2015-08-23 10:31 1.5K microsat.txt.gz 2015-08-23 10:31 275K mrnaOrientInfo.sql 2020-08-20 21:06 1.8K mrnaOrientInfo.txt.gz 2020-08-20 21:06 583K nestedRepeats.sql 2014-12-17 12:32 1.9K nestedRepeats.txt.gz 2014-12-17 12:32 16M netEquCab2.sql 2015-02-24 11:01 2.1K netEquCab2.txt.gz 2015-02-24 11:02 54M netHg38.sql 2014-12-17 12:32 2.1K netHg38.txt.gz 2014-12-17 12:32 66M netMm10.sql 2014-12-17 12:32 2.1K netMm10.txt.gz 2014-12-17 12:33 54M netRn6.sql 2017-03-26 13:29 2.1K netRn6.txt.gz 2017-03-26 13:30 54M refFlat.sql 2020-08-20 21:06 1.7K refFlat.txt.gz 2020-08-20 21:06 1.4M refGene.sql 2020-08-20 21:06 1.9K refGene.txt.gz 2020-08-20 21:06 1.5M refSeqAli.sql 2020-08-20 21:06 2.1K refSeqAli.txt.gz 2020-08-20 21:06 1.5M rmsk.sql 2014-12-17 12:33 1.9K rmsk.txt.gz 2014-12-17 12:33 141M sgpGene.sql 2015-08-30 18:40 1.9K sgpGene.txt.gz 2015-08-30 18:40 2.4M simpleRepeat.sql 2014-12-17 12:34 1.9K simpleRepeat.txt.gz 2014-12-17 12:34 12M snp148.sql 2016-09-25 05:32 3.0K snp148.txt.gz 2016-09-25 05:37 1.6G snp148CodingDbSnp.sql 2016-09-25 05:29 1.7K snp148CodingDbSnp.txt.gz 2016-09-25 05:29 82M snp148ExceptionDesc.sql 2016-09-25 05:30 1.4K snp148ExceptionDesc.txt.gz 2016-09-25 05:30 1.0K snp148Mult.sql 2016-09-25 05:44 3.0K snp148Mult.txt.gz 2016-09-25 05:44 2.0M snp148Seq.sql 2016-09-25 05:30 1.3K snp148Seq.txt.gz 2016-09-25 05:30 601M tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 6.7K tableList.sql 2022-06-19 03:06 1.6K tableList.txt.gz 2022-06-19 03:06 3.9K trackDb.sql 2021-12-17 16:15 2.1K trackDb.txt.gz 2021-12-17 16:15 50K ucscToINSDC.sql 2014-12-17 12:34 1.4K ucscToINSDC.txt.gz 2014-12-17 12:34 22K ucscToRefSeq.sql 2018-02-18 05:20 1.4K ucscToRefSeq.txt.gz 2018-02-18 05:20 24K windowmaskerSdust.sql 2014-12-17 12:34 1.5K windowmaskerSdust.txt.gz 2014-12-17 12:34 120M xenoRefFlat.sql 2020-08-20 21:06 1.7K xenoRefFlat.txt.gz 2020-08-20 21:06 29M xenoRefGene.sql 2020-08-20 21:06 1.9K xenoRefGene.txt.gz 2020-08-20 21:06 32M xenoRefSeqAli.sql 2020-08-20 21:06 2.1K xenoRefSeqAli.txt.gz 2020-08-20 21:06 32M