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;'

-----------------------------------------------------------------------------
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 - nestedRepeats.sql 2019-06-07 10:37 1.9K nestedRepeats.txt.gz 2019-06-07 10:37 16M all_mrna.sql 2019-06-07 10:37 2.1K all_mrna.txt.gz 2019-06-07 10:37 1.5M augustusGene.sql 2019-06-07 10:37 1.9K augustusGene.txt.gz 2019-06-07 10:37 2.3M mrnaOrientInfo.sql 2019-06-07 10:37 1.8K mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K netHg38.sql 2019-06-07 10:37 2.1K netHg38.txt.gz 2019-06-07 10:38 65M chainHg38.sql 2019-06-07 10:38 1.7K chainHg38.txt.gz 2019-06-07 10:38 156M chainHg38Link.sql 2019-06-07 10:39 1.5K chainHg38Link.txt.gz 2019-06-07 10:40 796M netMm10.sql 2019-06-07 10:43 2.1K netMm10.txt.gz 2019-06-07 10:43 55M chainMm10.sql 2019-06-07 10:43 1.7K chainMm10.txt.gz 2019-06-07 10:43 64M chainMm10Link.sql 2019-06-07 10:43 1.5K chainMm10Link.txt.gz 2019-06-07 10:44 495M chromInfo.sql 2019-06-07 10:46 1.4K chromInfo.txt.gz 2019-06-07 10:46 14K cpgIslandExt.sql 2019-06-07 10:46 1.7K cpgIslandExt.txt.gz 2019-06-07 10:46 815K refFlat.sql 2019-06-07 10:46 1.7K refFlat.txt.gz 2019-06-07 10:46 1.3M cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K grp.sql 2019-06-07 10:46 1.3K grp.txt.gz 2019-06-07 10:46 213 cytoBandIdeo.sql 2019-06-07 10:46 1.5K cytoBandIdeo.txt.gz 2019-06-07 10:46 13K gap.sql 2019-06-07 10:46 1.6K gap.txt.gz 2019-06-07 10:46 28 gc5BaseBw.sql 2019-06-07 10:46 1.3K gc5BaseBw.txt.gz 2019-06-07 10:46 66 refGene.sql 2019-06-07 10:46 1.9K refGene.txt.gz 2019-06-07 10:46 1.4M refSeqAli.sql 2019-06-07 10:46 2.1K refSeqAli.txt.gz 2019-06-07 10:46 1.4M rmsk.sql 2019-06-07 10:46 1.9K rmsk.txt.gz 2019-06-07 10:46 142M genscan.sql 2019-06-07 10:47 1.7K genscan.txt.gz 2019-06-07 10:47 3.0M gold.sql 2019-06-07 10:47 1.7K gold.txt.gz 2019-06-07 10:47 27K simpleRepeat.sql 2019-06-07 10:47 1.9K simpleRepeat.txt.gz 2019-06-07 10:47 15M history.sql 2019-06-07 10:47 1.6K history.txt.gz 2019-06-07 10:47 912 microsat.sql 2019-06-07 10:47 1.5K microsat.txt.gz 2019-06-07 10:47 278K ucscToINSDC.sql 2019-06-07 10:47 1.4K ucscToINSDC.txt.gz 2019-06-07 10:47 20K ucscToRefSeq.sql 2019-06-07 10:47 1.4K ucscToRefSeq.txt.gz 2019-06-07 10:47 19K windowmaskerSdust.sql 2019-06-07 10:47 1.5K windowmaskerSdust.txt.gz 2019-06-07 10:47 119M xenoRefFlat.sql 2019-06-07 10:47 1.7K xenoRefFlat.txt.gz 2019-06-07 10:47 20M xenoRefGene.sql 2019-06-07 10:47 1.9K xenoRefGene.txt.gz 2019-06-07 10:47 21M xenoRefSeqAli.sql 2019-06-07 10:47 2.1K xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M all_est.sql 2019-06-16 03:21 2.1K all_est.txt.gz 2019-06-16 03:21 58M estOrientInfo.sql 2019-06-16 03:21 1.8K estOrientInfo.txt.gz 2019-06-16 03:21 18M gbLoaded.sql 2019-06-16 03:21 1.6K gbLoaded.txt.gz 2019-06-16 03:21 4.2K intronEst.sql 2019-06-16 03:21 2.1K intronEst.txt.gz 2019-06-16 03:21 37M chromAlias.sql 2020-04-12 03:25 1.4K chromAlias.txt.gz 2020-04-12 03:25 21K ncbiRefSeq.sql 2020-05-10 03:26 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.3M 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 13M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M extNcbiRefSeq.sql 2020-05-10 03:26 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:26 89 ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M chainMm39.sql 2020-11-23 19:20 1.7K chainMm39.txt.gz 2020-11-23 19:20 68M chainMm39Link.sql 2020-11-23 19:23 1.6K chainMm39Link.txt.gz 2020-11-23 19:23 502M netMm39.sql 2020-11-23 19:26 2.1K netMm39.txt.gz 2020-11-23 19:26 55M ensGene.sql 2021-05-25 14:20 1.9K ensGene.txt.gz 2021-05-25 14:20 2.9M ensGtp.sql 2021-05-25 14:20 1.4K ensGtp.txt.gz 2021-05-25 14:20 507K ensemblToGeneName.sql 2021-05-25 14:20 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:20 245K ensemblSource.sql 2021-05-25 14:22 1.4K ensemblSource.txt.gz 2021-05-25 14:22 134K ensPep.sql 2021-05-25 14:22 1.3K ensPep.txt.gz 2021-05-25 14:22 13M crisprAllTargets.sql 2022-03-20 13:48 1.3K crisprAllTargets.txt.gz 2022-03-20 13:48 69 trackDb_pushedout.sql 2023-12-20 15:31 2.1K trackDb_pushedout.txt.gz 2023-12-20 15:31 60K hgFindSpec_pushedout.sql 2023-12-20 15:31 1.8K hgFindSpec_pushedout.txt.gz 2023-12-20 15:31 1.3K trackDb.sql 2024-01-31 15:13 2.1K trackDb.txt.gz 2024-01-31 15:13 60K hgFindSpec.sql 2024-01-31 15:13 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 1.3K tableDescriptions.sql 2024-03-23 02:04 1.4K tableDescriptions.txt.gz 2024-03-23 02:04 6.3K tableList.sql 2024-03-24 03:07 1.6K tableList.txt.gz 2024-03-24 03:07 3.6K bigFiles.sql 2024-03-24 03:07 1.4K bigFiles.txt.gz 2024-03-24 03:07 119