This directory contains a dump of the UCSC genome annotation database for
the Oct. 2007 assembly of the cow genome (bosTau4, Baylor Release 4.0).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Baylor College of Medicine Human Genome Sequencing Center.
For more information on the cow genome, see the project website:
<A HREF="http://www.hgsc.bcm.tmc.edu/projects/bovine/"
TARGET=_blank>Baylor College of Medicine Human Genome Sequencing Center</A>

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=bosTau4
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/bosTau4/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/bosTau4/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/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 bosTau4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bosTau4 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

For conditions of use regarding the Cow genome sequence data, see
http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html .

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

      Name                         Last modified      Size  Description
Parent Directory - all_est.sql 2016-06-05 09:04 2.1K all_est.txt.gz 2016-06-05 09:04 64M all_mrna.sql 2020-08-20 21:48 2.1K all_mrna.txt.gz 2020-08-20 21:48 1.6M augustusGene.sql 2015-07-26 10:13 1.9K augustusGene.txt.gz 2015-07-26 10:13 2.3M bigFiles.sql 2022-06-26 03:08 1.4K bigFiles.txt.gz 2022-06-26 03:08 33 blastHg18KG.sql 2009-12-20 10:21 2.3K blastHg18KG.txt.gz 2009-12-20 10:21 4.0M chainCanFam2.sql 2008-04-07 12:14 1.7K chainCanFam2.txt.gz 2008-04-07 12:17 74M chainCanFam2Link.sql 2008-04-07 12:20 1.4K chainCanFam2Link.txt.gz 2008-04-07 12:48 670M chainHg19.sql 2009-09-20 07:33 1.8K chainHg19.txt.gz 2009-09-20 07:33 234M chainHg19Link.sql 2009-09-20 07:34 1.5K chainHg19Link.txt.gz 2009-09-20 07:36 968M chainMm9.sql 2008-04-07 14:17 1.6K chainMm9.txt.gz 2008-04-07 14:19 64M chainMm9Link.sql 2008-04-07 14:20 1.4K chainMm9Link.txt.gz 2008-04-07 14:35 497M chainOrnAna1.sql 2008-04-07 14:49 1.7K chainOrnAna1.txt.gz 2008-04-07 14:50 45M chainOrnAna1Link.sql 2008-04-07 14:51 1.4K chainOrnAna1Link.txt.gz 2008-04-07 14:58 249M chainOviAri1.sql 2011-04-25 08:41 1.6K chainOviAri1.txt.gz 2011-04-25 08:52 2.3G chainOviAri1Link.sql 2011-04-25 07:32 1.5K chainOviAri1Link.txt.gz 2011-04-25 07:49 4.3G chainSusScr2.sql 2010-05-16 11:01 1.6K chainSusScr2.txt.gz 2010-05-16 11:07 3.0G chainSusScr2Link.sql 2010-05-16 11:22 1.5K chainSusScr2Link.txt.gz 2010-05-16 11:47 12G chromInfo.sql 2008-04-07 15:04 1.2K chromInfo.txt.gz 2008-04-07 15:04 60K cpgIslandExt.sql 2008-04-07 15:04 1.6K cpgIslandExt.txt.gz 2008-04-07 15:04 805K cpgIslandExtUnmasked.sql 2014-06-01 08:32 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:32 889K cytoBandIdeo.sql 2013-08-11 03:45 1.5K cytoBandIdeo.txt.gz 2013-08-11 03:45 56K ensGene.sql 2011-03-14 08:23 1.9K ensGene.txt.gz 2011-03-14 08:23 2.4M ensGtp.sql 2011-03-14 08:23 1.4K ensGtp.txt.gz 2011-03-14 08:23 323K ensPep.sql 2011-03-14 08:25 1.3K ensPep.txt.gz 2011-03-14 08:25 7.3M ensemblSource.sql 2011-10-03 07:42 1.3K ensemblSource.txt.gz 2011-10-03 07:42 119K ensemblToGeneName.sql 2011-10-03 07:42 1.3K ensemblToGeneName.txt.gz 2011-10-03 07:42 199K estOrientInfo.sql 2016-06-05 09:04 1.8K estOrientInfo.txt.gz 2016-06-05 09:04 20M extFile.sql 2008-04-07 14:51 1.3K extFile.txt.gz 2008-04-07 14:51 85 gap.sql 2008-04-07 15:04 1.5K gap.txt.gz 2008-04-07 15:04 1.0M gbLoaded.sql 2020-08-20 21:54 1.6K gbLoaded.txt.gz 2020-08-20 21:54 43K gc5Base.sql 2008-04-07 15:09 1.7K gc5Base.txt.gz 2008-04-07 15:10 11M genscan.sql 2008-04-07 15:10 1.6K genscan.txt.gz 2008-04-07 15:10 3.2M genscanPep.sql 2010-10-31 13:25 1.3K genscanPep.txt.gz 2010-10-31 13:25 11M gold.sql 2008-04-07 15:10 1.6K gold.txt.gz 2008-04-07 15:10 2.3M grp.sql 2014-03-02 03:37 1.4K grp.txt.gz 2014-03-02 03:37 208 hgFindSpec.sql 2021-12-27 12:21 1.8K hgFindSpec.txt.gz 2021-12-27 12:21 951 history.sql 2008-04-07 15:10 1.4K history.txt.gz 2008-04-07 15:10 742 intronEst.sql 2016-06-05 09:03 2.1K intronEst.txt.gz 2016-06-05 09:03 37M mgcFullMrna.sql 2020-03-01 04:52 2.1K mgcFullMrna.txt.gz 2020-03-01 04:52 908K mgcGenes.sql 2020-03-01 04:52 1.9K mgcGenes.txt.gz 2020-03-01 04:52 803K microsat.sql 2015-08-23 10:14 1.5K microsat.txt.gz 2015-08-23 10:14 299K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K mrnaOrientInfo.txt.gz 2020-08-20 21:48 591K multiz5way.sql 2008-04-07 15:16 1.4K multiz5way.txt.gz 2008-04-07 15:19 91M multiz5wayFrames.sql 2008-04-07 15:21 1.7K multiz5wayFrames.txt.gz 2008-04-07 15:21 7.7M multiz5waySummary.sql 2008-04-07 15:21 1.5K multiz5waySummary.txt.gz 2008-04-07 15:21 9.8M nestedRepeats.sql 2008-04-07 15:21 1.9K nestedRepeats.txt.gz 2008-04-07 15:22 15M netCanFam2.sql 2008-04-07 15:22 2.2K netCanFam2.txt.gz 2008-04-07 15:25 73M netHg19.sql 2009-09-20 07:41 2.3K netHg19.txt.gz 2009-09-20 07:41 68M netMm9.sql 2008-04-07 15:12 2.2K netMm9.txt.gz 2008-04-07 15:15 56M netOrnAna1.sql 2008-04-07 15:30 2.2K netOrnAna1.txt.gz 2008-04-07 15:31 18M netOviAri1.sql 2011-04-25 07:31 2.0K netOviAri1.txt.gz 2011-04-25 07:31 80M netSusScr2.sql 2010-05-16 11:22 2.0K netSusScr2.txt.gz 2010-05-16 11:22 73M nscanGene.sql 2008-04-25 03:16 1.9K nscanGene.txt.gz 2008-04-25 03:16 1.4M nscanPep.sql 2008-04-25 03:16 1.1K nscanPep.txt.gz 2008-04-25 03:16 5.1M phastCons5way.sql 2008-04-07 15:31 1.7K phastCons5way.txt.gz 2008-04-07 15:34 70M phastConsElements5way.sql 2008-04-07 15:36 1.4K phastConsElements5way.txt.gz 2008-04-07 15:36 9.8M quality.sql 2008-04-07 15:36 1.7K quality.txt.gz 2008-04-07 15:39 58M refFlat.sql 2020-08-20 21:48 1.7K refFlat.txt.gz 2020-08-20 21:48 1.4M refGene.sql 2020-08-20 21:48 1.9K refGene.txt.gz 2020-08-20 21:48 1.5M refSeqAli.sql 2020-08-20 21:48 2.1K refSeqAli.txt.gz 2020-08-20 21:48 1.5M rmsk.sql 2008-04-07 15:40 1.9K rmsk.txt.gz 2008-04-07 15:43 135M simpleRepeat.sql 2008-04-07 15:46 1.9K simpleRepeat.txt.gz 2008-04-07 15:46 12M tRNAs.sql 2012-04-22 18:28 1.7K tRNAs.txt.gz 2012-04-22 18:28 109K tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 6.6K tableList.sql 2022-06-26 03:08 1.6K tableList.txt.gz 2022-06-26 03:08 4.2K trackDb.sql 2021-12-27 12:21 2.1K trackDb.txt.gz 2021-12-27 12:21 49K wgEncodeNhgriBip.sql 2009-08-02 05:56 1.7K wgEncodeNhgriBip.txt.gz 2009-08-02 05:56 11K xenoMrna.sql 2016-02-21 10:02 2.1K xenoMrna.txt.gz 2016-02-21 10:04 309M xenoRefFlat.sql 2020-08-20 21:48 1.7K xenoRefFlat.txt.gz 2020-08-20 21:48 29M xenoRefGene.sql 2020-08-20 21:48 1.9K xenoRefGene.txt.gz 2020-08-20 21:48 32M xenoRefSeqAli.sql 2020-08-20 21:48 2.1K xenoRefSeqAli.txt.gz 2020-08-20 21:48 31M