This directory contains a dump of the UCSC genome annotation database for the
    Apr. 2018 (ARS-UCD1.2/bosTau9) assembly of the cow genome
    (bosTau9, USDA ARS) .

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    https://www.ncbi.nlm.nih.gov/genome/82
    https://www.ncbi.nlm.nih.gov/genome/assembly/1677391
    https://www.ncbi.nlm.nih.gov/bioproject/391427

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=bosTau9
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.soe.ucsc.edu, then go to
the directory goldenPath/bosTau9/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.soe.ucsc.edu/goldenPath/bosTau9/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

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 bosTau9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau9 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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

      Name                        Last modified      Size  Description
Parent Directory - xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M xenoRefSeqAli.sql 2019-06-07 10:47 2.1K xenoRefGene.txt.gz 2019-06-07 10:47 21M xenoRefGene.sql 2019-06-07 10:47 1.9K xenoRefFlat.txt.gz 2019-06-07 10:47 20M xenoRefFlat.sql 2019-06-07 10:47 1.7K windowmaskerSdust.txt.gz 2019-06-07 10:47 119M windowmaskerSdust.sql 2019-06-07 10:47 1.5K ucscToRefSeq.txt.gz 2019-06-07 10:47 19K ucscToRefSeq.sql 2019-06-07 10:47 1.4K ucscToINSDC.txt.gz 2019-06-07 10:47 20K ucscToINSDC.sql 2019-06-07 10:47 1.4K trackDb_pushedout.txt.gz 2023-12-20 15:31 60K trackDb_pushedout.sql 2023-12-20 15:31 2.1K trackDb.txt.gz 2024-01-31 15:13 60K trackDb.sql 2024-01-31 15:13 2.1K tableList.txt.gz 2024-03-03 03:08 3.6K tableList.sql 2024-03-03 03:08 1.6K tableDescriptions.txt.gz 2024-03-02 02:13 6.3K tableDescriptions.sql 2024-03-02 02:13 1.4K simpleRepeat.txt.gz 2019-06-07 10:47 15M simpleRepeat.sql 2019-06-07 10:47 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K rmsk.txt.gz 2019-06-07 10:46 142M rmsk.sql 2019-06-07 10:46 1.9K refSeqAli.txt.gz 2019-06-07 10:46 1.4M refSeqAli.sql 2019-06-07 10:46 2.1K refGene.txt.gz 2019-06-07 10:46 1.4M refGene.sql 2019-06-07 10:46 1.9K refFlat.txt.gz 2019-06-07 10:46 1.3M refFlat.sql 2019-06-07 10:46 1.7K netMm39.txt.gz 2020-11-23 19:26 55M netMm39.sql 2020-11-23 19:26 2.1K netMm10.txt.gz 2019-06-07 10:43 55M netMm10.sql 2019-06-07 10:43 2.1K netHg38.txt.gz 2019-06-07 10:38 65M netHg38.sql 2019-06-07 10:37 2.1K nestedRepeats.txt.gz 2019-06-07 10:37 16M nestedRepeats.sql 2019-06-07 10:37 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 13M 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 2.3M ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeq.sql 2020-05-10 03:26 1.9K mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K mrnaOrientInfo.sql 2019-06-07 10:37 1.8K microsat.txt.gz 2019-06-07 10:47 278K microsat.sql 2019-06-07 10:47 1.5K intronEst.txt.gz 2019-06-16 03:21 37M intronEst.sql 2019-06-16 03:21 2.1K history.txt.gz 2019-06-07 10:47 912 history.sql 2019-06-07 10:47 1.6K hgFindSpec_pushedout.txt.gz 2023-12-20 15:31 1.3K hgFindSpec_pushedout.sql 2023-12-20 15:31 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 1.3K hgFindSpec.sql 2024-01-31 15:13 1.8K grp.txt.gz 2019-06-07 10:46 213 grp.sql 2019-06-07 10:46 1.3K gold.txt.gz 2019-06-07 10:47 27K gold.sql 2019-06-07 10:47 1.7K genscan.txt.gz 2019-06-07 10:47 3.0M genscan.sql 2019-06-07 10:47 1.7K gc5BaseBw.txt.gz 2019-06-07 10:46 66 gc5BaseBw.sql 2019-06-07 10:46 1.3K gbLoaded.txt.gz 2019-06-16 03:21 4.2K gbLoaded.sql 2019-06-16 03:21 1.6K gap.txt.gz 2019-06-07 10:46 28 gap.sql 2019-06-07 10:46 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:26 89 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K estOrientInfo.txt.gz 2019-06-16 03:21 18M estOrientInfo.sql 2019-06-16 03:21 1.8K ensemblToGeneName.txt.gz 2021-05-25 14:20 245K ensemblToGeneName.sql 2021-05-25 14:20 1.4K ensemblSource.txt.gz 2021-05-25 14:22 134K ensemblSource.sql 2021-05-25 14:22 1.4K ensPep.txt.gz 2021-05-25 14:22 13M ensPep.sql 2021-05-25 14:22 1.3K ensGtp.txt.gz 2021-05-25 14:20 507K ensGtp.sql 2021-05-25 14:20 1.4K ensGene.txt.gz 2021-05-25 14:20 2.9M ensGene.sql 2021-05-25 14:20 1.9K cytoBandIdeo.txt.gz 2019-06-07 10:46 13K cytoBandIdeo.sql 2019-06-07 10:46 1.5K crisprAllTargets.txt.gz 2022-03-20 13:48 69 crisprAllTargets.sql 2022-03-20 13:48 1.3K cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K cpgIslandExt.txt.gz 2019-06-07 10:46 815K cpgIslandExt.sql 2019-06-07 10:46 1.7K chromInfo.txt.gz 2019-06-07 10:46 14K chromInfo.sql 2019-06-07 10:46 1.4K chromAlias.txt.gz 2020-04-12 03:25 21K chromAlias.sql 2020-04-12 03:25 1.4K chainMm39Link.txt.gz 2020-11-23 19:23 502M chainMm39Link.sql 2020-11-23 19:23 1.6K chainMm39.txt.gz 2020-11-23 19:20 68M chainMm39.sql 2020-11-23 19:20 1.7K chainMm10Link.txt.gz 2019-06-07 10:44 495M chainMm10Link.sql 2019-06-07 10:43 1.5K chainMm10.txt.gz 2019-06-07 10:43 64M chainMm10.sql 2019-06-07 10:43 1.7K chainHg38Link.txt.gz 2019-06-07 10:40 796M chainHg38Link.sql 2019-06-07 10:39 1.5K chainHg38.txt.gz 2019-06-07 10:38 156M chainHg38.sql 2019-06-07 10:38 1.7K bigFiles.txt.gz 2024-03-03 03:08 119 bigFiles.sql 2024-03-03 03:08 1.4K augustusGene.txt.gz 2019-06-07 10:37 2.3M augustusGene.sql 2019-06-07 10:37 1.9K all_mrna.txt.gz 2019-06-07 10:37 1.5M all_mrna.sql 2019-06-07 10:37 2.1K all_est.txt.gz 2019-06-16 03:21 58M all_est.sql 2019-06-16 03:21 2.1K