This directory contains a dump of the UCSC genome annotation database for
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly of the cow genome (bosTau6, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the cow genome, see the project website:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10708

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=bosTau6
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/bosTau6/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/bosTau6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/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 bosTau6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau6 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'


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

      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2011-11-02 12:13 63 bamAllNumtSSorted.txt.gz 2013-08-18 03:44 85 bigFiles.txt.gz 2022-08-07 03:10 109 grp.txt.gz 2014-03-02 03:37 208 history.txt.gz 2011-11-02 15:21 608 hgFindSpec.txt.gz 2021-12-27 12:20 829 gc5BaseBw.sql 2011-11-02 12:13 1.2K ucscToEnsembl.sql 2011-11-02 12:36 1.3K bamAllNumtSSorted.sql 2013-08-18 03:44 1.3K chromInfo.sql 2011-11-02 16:11 1.3K ensPep.sql 2018-08-05 05:24 1.3K grp.sql 2014-03-02 03:37 1.3K ensemblSource.sql 2018-08-05 05:24 1.4K bigFiles.sql 2022-08-07 03:10 1.4K ensemblToGeneName.sql 2018-08-05 05:27 1.4K ensGtp.sql 2018-08-05 05:24 1.4K chromAlias.sql 2018-08-05 05:27 1.4K tableDescriptions.sql 2021-01-14 06:34 1.4K chainMm9Link.sql 2011-11-02 15:56 1.5K chainRn4Link.sql 2011-11-02 15:43 1.5K chainHg19Link.sql 2011-11-02 15:21 1.5K ctgPos2.sql 2011-11-02 15:38 1.5K chainCanFam2Link.sql 2011-11-02 12:13 1.5K chainMonDom5Link.sql 2011-11-02 11:46 1.5K chainOrnAna1Link.sql 2011-11-02 15:10 1.5K chainSusScr2Link.sql 2011-11-02 12:36 1.5K microsat.sql 2015-08-23 10:22 1.5K history.sql 2011-11-02 15:21 1.5K cytoBandIdeo.sql 2013-08-11 03:45 1.5K gap.sql 2011-11-02 15:21 1.5K tableList.sql 2022-08-07 03:10 1.6K gbLoaded.sql 2020-08-20 21:48 1.6K numtSMitochondrion.sql 2013-08-18 03:44 1.6K gold.sql 2011-11-02 15:52 1.6K cpgIslandExt.sql 2011-11-02 15:09 1.6K chainMm9.sql 2011-11-02 11:05 1.6K chainRn4.sql 2011-11-02 15:38 1.6K chainHg19.sql 2011-11-02 11:01 1.6K chainCanFam2.sql 2011-11-02 16:10 1.6K chainMonDom5.sql 2011-11-02 15:39 1.6K chainOrnAna1.sql 2011-11-02 11:07 1.6K chainSusScr2.sql 2011-11-02 11:08 1.6K tRNAs.sql 2012-04-15 15:40 1.7K refFlat.sql 2020-08-20 21:48 1.7K cpgIslandExtUnmasked.sql 2014-06-01 08:38 1.7K xenoRefFlat.sql 2020-08-20 21:48 1.7K numtS.sql 2013-08-18 03:44 1.7K hgFindSpec.sql 2021-12-27 12:20 1.8K estOrientInfo.sql 2016-06-19 05:20 1.8K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K rmsk.sql 2011-11-02 15:15 1.8K numtSAssembled.sql 2013-08-18 03:44 1.8K simpleRepeat.sql 2011-11-02 15:09 1.9K nestedRepeats.sql 2011-11-02 12:36 1.9K ensGene.sql 2018-08-05 05:27 1.9K refGene.sql 2020-08-20 21:48 1.9K xenoRefGene.sql 2020-08-20 21:48 1.9K augustusGene.sql 2015-07-26 10:13 1.9K netMm9.sql 2011-11-02 15:17 2.0K netRn4.sql 2011-11-02 16:07 2.0K netHg19.sql 2011-11-02 15:09 2.0K netCanFam2.sql 2011-11-02 12:11 2.0K netMonDom5.sql 2011-11-02 15:19 2.0K netOrnAna1.sql 2011-11-02 16:08 2.0K netSusScr2.sql 2011-11-02 16:08 2.0K trackDb.sql 2021-12-27 12:20 2.1K all_est.sql 2016-06-19 05:20 2.1K all_mrna.sql 2020-08-20 21:43 2.1K xenoMrna.sql 2020-08-20 21:43 2.1K intronEst.sql 2016-06-19 05:20 2.1K refSeqAli.sql 2020-08-20 21:48 2.1K xenoRefSeqAli.sql 2020-08-20 21:48 2.1K numtSMitochondrion.txt.gz 2013-08-18 03:44 2.4K numtSAssembled.txt.gz 2013-08-18 03:44 2.7K tableList.txt.gz 2022-08-07 03:10 3.6K tableDescriptions.txt.gz 2021-01-14 06:34 6.1K numtS.txt.gz 2013-08-18 03:44 8.8K chromAlias.txt.gz 2018-08-05 05:27 14K chromInfo.txt.gz 2011-11-02 16:11 16K cytoBandIdeo.txt.gz 2013-08-11 03:45 16K ucscToEnsembl.txt.gz 2011-11-02 12:36 19K trackDb.txt.gz 2021-12-27 12:20 37K ctgPos2.txt.gz 2011-11-02 15:38 47K ensemblSource.txt.gz 2018-08-05 05:24 86K tRNAs.txt.gz 2012-04-15 15:40 107K gbLoaded.txt.gz 2020-08-20 21:48 107K ensemblToGeneName.txt.gz 2018-08-05 05:27 168K microsat.txt.gz 2015-08-23 10:22 275K ensGtp.txt.gz 2018-08-05 05:24 311K mrnaOrientInfo.txt.gz 2020-08-20 21:48 595K cpgIslandExt.txt.gz 2011-11-02 15:09 811K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:38 924K gap.txt.gz 2011-11-02 15:21 1.0M gold.txt.gz 2011-11-02 15:52 1.3M refFlat.txt.gz 2020-08-20 21:48 1.4M refGene.txt.gz 2020-08-20 21:48 1.5M refSeqAli.txt.gz 2020-08-20 21:48 1.5M all_mrna.txt.gz 2020-08-20 21:43 1.6M ensGene.txt.gz 2018-08-05 05:27 2.3M augustusGene.txt.gz 2015-07-26 10:13 2.3M ensPep.txt.gz 2018-08-05 05:24 6.7M simpleRepeat.txt.gz 2011-11-02 15:09 12M nestedRepeats.txt.gz 2011-11-02 12:36 15M netMonDom5.txt.gz 2011-11-02 15:19 17M netOrnAna1.txt.gz 2011-11-02 16:08 17M estOrientInfo.txt.gz 2016-06-19 05:20 19M xenoRefFlat.txt.gz 2020-08-20 21:48 29M xenoRefGene.txt.gz 2020-08-20 21:48 32M xenoRefSeqAli.txt.gz 2020-08-20 21:48 34M intronEst.txt.gz 2016-06-19 05:21 37M chainOrnAna1.txt.gz 2011-11-02 11:07 41M netRn4.txt.gz 2011-11-02 16:08 52M netMm9.txt.gz 2011-11-02 15:18 54M chainRn4.txt.gz 2011-11-02 15:39 55M all_est.txt.gz 2016-06-19 05:20 62M chainMm9.txt.gz 2011-11-02 11:06 64M netSusScr2.txt.gz 2011-11-02 16:09 65M netHg19.txt.gz 2011-11-02 15:09 66M netCanFam2.txt.gz 2011-11-02 12:12 71M chainCanFam2.txt.gz 2011-11-02 16:10 71M rmsk.txt.gz 2011-11-02 15:15 135M chainHg19.txt.gz 2011-11-02 11:02 180M chainMonDom5.txt.gz 2011-11-02 15:40 210M chainOrnAna1Link.txt.gz 2011-11-02 15:11 234M xenoMrna.txt.gz 2020-08-20 21:43 346M chainRn4Link.txt.gz 2011-11-02 15:46 455M chainMm9Link.txt.gz 2011-11-02 15:59 491M chainCanFam2Link.txt.gz 2011-11-02 12:18 650M chainMonDom5Link.txt.gz 2011-11-02 11:50 656M chainHg19Link.txt.gz 2011-11-02 15:26 835M chainSusScr2.txt.gz 2011-11-02 11:24 1.4G chainSusScr2Link.txt.gz 2011-11-02 13:33 6.9G