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 - xenoRefSeqAli.txt.gz 2020-08-20 21:48 31M xenoRefSeqAli.sql 2020-08-20 21:48 2.1K xenoRefGene.txt.gz 2020-08-20 21:48 32M xenoRefGene.sql 2020-08-20 21:48 2.0K xenoRefFlat.txt.gz 2020-08-20 21:48 29M xenoRefFlat.sql 2020-08-20 21:48 1.7K xenoMrna.txt.gz 2016-02-21 10:04 309M xenoMrna.sql 2016-02-21 10:02 2.1K wgEncodeNhgriBip.txt.gz 2009-08-02 05:56 11K wgEncodeNhgriBip.sql 2009-08-02 05:56 1.7K trackDb_pushedout.txt.gz 2021-12-27 12:21 49K trackDb_pushedout.sql 2021-12-27 12:21 2.1K trackDb.txt.gz 2023-03-28 13:46 50K trackDb.sql 2023-03-28 13:46 2.1K tableList.txt.gz 2024-04-14 03:20 4.3K tableList.sql 2024-04-14 03:20 1.6K tableDescriptions.txt.gz 2024-04-13 02:03 6.8K tableDescriptions.sql 2024-04-13 02:03 1.4K tRNAs.txt.gz 2012-04-22 18:28 109K tRNAs.sql 2012-04-22 18:28 1.7K simpleRepeat.txt.gz 2008-04-07 15:46 12M simpleRepeat.sql 2008-04-07 15:46 1.9K rmsk.txt.gz 2008-04-07 15:43 135M rmsk.sql 2008-04-07 15:40 1.9K refSeqAli.txt.gz 2020-08-20 21:48 1.5M refSeqAli.sql 2020-08-20 21:48 2.1K refGene.txt.gz 2020-08-20 21:48 1.5M refGene.sql 2020-08-20 21:48 1.9K refFlat.txt.gz 2020-08-20 21:48 1.4M refFlat.sql 2020-08-20 21:48 1.7K quality.txt.gz 2008-04-07 15:39 58M quality.sql 2008-04-07 15:36 1.7K phastConsElements5way.txt.gz 2008-04-07 15:36 9.8M phastConsElements5way.sql 2008-04-07 15:36 1.4K phastCons5way.txt.gz 2008-04-07 15:34 70M phastCons5way.sql 2008-04-07 15:31 1.7K nscanPep.txt.gz 2008-04-25 03:16 5.1M nscanPep.sql 2008-04-25 03:16 1.1K nscanGene.txt.gz 2008-04-25 03:16 1.4M nscanGene.sql 2008-04-25 03:16 1.9K netSusScr2.txt.gz 2010-05-16 11:22 73M netSusScr2.sql 2010-05-16 11:22 2.0K netOviAri1.txt.gz 2011-04-25 07:31 80M netOviAri1.sql 2011-04-25 07:31 2.0K netOrnAna1.txt.gz 2008-04-07 15:31 18M netOrnAna1.sql 2008-04-07 15:30 2.2K netMm9.txt.gz 2008-04-07 15:15 56M netMm9.sql 2008-04-07 15:12 2.2K netHg19.txt.gz 2009-09-20 07:41 68M netHg19.sql 2009-09-20 07:41 2.3K netCanFam2.txt.gz 2008-04-07 15:25 73M netCanFam2.sql 2008-04-07 15:22 2.2K nestedRepeats.txt.gz 2008-04-07 15:22 15M nestedRepeats.sql 2008-04-07 15:21 1.9K multiz5waySummary.txt.gz 2008-04-07 15:21 9.8M multiz5waySummary.sql 2008-04-07 15:21 1.5K multiz5wayFrames.txt.gz 2008-04-07 15:21 7.7M multiz5wayFrames.sql 2008-04-07 15:21 1.7K multiz5way.txt.gz 2008-04-07 15:19 91M multiz5way.sql 2008-04-07 15:16 1.4K mrnaOrientInfo.txt.gz 2020-08-20 21:48 591K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K microsat.txt.gz 2015-08-23 10:14 299K microsat.sql 2015-08-23 10:14 1.5K mgcGenes.txt.gz 2020-03-01 04:52 803K mgcGenes.sql 2020-03-01 04:52 1.9K mgcFullMrna.txt.gz 2020-03-01 04:52 908K mgcFullMrna.sql 2020-03-01 04:52 2.1K intronEst.txt.gz 2016-06-05 09:03 37M intronEst.sql 2016-06-05 09:03 2.1K history.txt.gz 2008-04-07 15:10 742 history.sql 2008-04-07 15:10 1.4K hgFindSpec_pushedout.txt.gz 2021-12-27 12:21 961 hgFindSpec_pushedout.sql 2021-12-27 12:21 1.8K hgFindSpec.txt.gz 2023-03-28 13:46 1.0K hgFindSpec.sql 2023-03-28 13:46 1.8K grp.txt.gz 2014-03-02 03:37 208 grp.sql 2014-03-02 03:37 1.4K gold.txt.gz 2008-04-07 15:10 2.3M gold.sql 2008-04-07 15:10 1.6K genscanPep.txt.gz 2010-10-31 13:25 11M genscanPep.sql 2010-10-31 13:25 1.3K genscan.txt.gz 2008-04-07 15:10 3.2M genscan.sql 2008-04-07 15:10 1.6K gc5Base.txt.gz 2008-04-07 15:10 11M gc5Base.sql 2008-04-07 15:09 1.7K gbLoaded.txt.gz 2020-08-20 21:54 43K gbLoaded.sql 2020-08-20 21:54 1.6K gap.txt.gz 2008-04-07 15:04 1.0M gap.sql 2008-04-07 15:04 1.5K extFile.txt.gz 2008-04-07 14:51 85 extFile.sql 2008-04-07 14:51 1.3K estOrientInfo.txt.gz 2016-06-05 09:04 20M estOrientInfo.sql 2016-06-05 09:04 1.8K ensemblToGeneName.txt.gz 2011-10-03 07:42 199K ensemblToGeneName.sql 2011-10-03 07:42 1.3K ensemblSource.txt.gz 2011-10-03 07:42 119K ensemblSource.sql 2011-10-03 07:42 1.3K ensPep.txt.gz 2011-03-14 08:25 7.3M ensPep.sql 2011-03-14 08:25 1.3K ensGtp.txt.gz 2011-03-14 08:23 323K ensGtp.sql 2011-03-14 08:23 1.4K ensGene.txt.gz 2011-03-14 08:23 2.4M ensGene.sql 2011-03-14 08:23 1.9K cytoBandIdeo.txt.gz 2013-08-11 03:45 56K cytoBandIdeo.sql 2013-08-11 03:45 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:32 889K cpgIslandExtUnmasked.sql 2014-06-01 08:32 1.7K cpgIslandExt.txt.gz 2008-04-07 15:04 805K cpgIslandExt.sql 2008-04-07 15:04 1.6K chromInfo.txt.gz 2008-04-07 15:04 60K chromInfo.sql 2008-04-07 15:04 1.2K chainSusScr2Link.txt.gz 2010-05-16 11:47 12G chainSusScr2Link.sql 2010-05-16 11:22 1.5K chainSusScr2.txt.gz 2010-05-16 11:07 3.0G chainSusScr2.sql 2010-05-16 11:01 1.6K chainOviAri1Link.txt.gz 2011-04-25 07:49 4.3G chainOviAri1Link.sql 2011-04-25 07:32 1.5K chainOviAri1.txt.gz 2011-04-25 08:52 2.3G chainOviAri1.sql 2011-04-25 08:41 1.6K chainOrnAna1Link.txt.gz 2008-04-07 14:58 249M chainOrnAna1Link.sql 2008-04-07 14:51 1.4K chainOrnAna1.txt.gz 2008-04-07 14:50 45M chainOrnAna1.sql 2008-04-07 14:49 1.7K chainMm9Link.txt.gz 2008-04-07 14:35 497M chainMm9Link.sql 2008-04-07 14:20 1.4K chainMm9.txt.gz 2008-04-07 14:19 64M chainMm9.sql 2008-04-07 14:17 1.6K chainHg19Link.txt.gz 2009-09-20 07:36 968M chainHg19Link.sql 2009-09-20 07:34 1.5K chainHg19.txt.gz 2009-09-20 07:33 234M chainHg19.sql 2009-09-20 07:33 1.8K chainCanFam2Link.txt.gz 2008-04-07 12:48 670M chainCanFam2Link.sql 2008-04-07 12:20 1.4K chainCanFam2.txt.gz 2008-04-07 12:17 74M chainCanFam2.sql 2008-04-07 12:14 1.7K blastHg18KG.txt.gz 2009-12-20 10:21 4.0M blastHg18KG.sql 2009-12-20 10:21 2.3K bigFiles.txt.gz 2024-04-14 03:20 33 bigFiles.sql 2024-04-14 03:20 1.4K augustusGene.txt.gz 2015-07-26 10:13 2.3M augustusGene.sql 2015-07-26 10:13 1.9K all_mrna.txt.gz 2020-08-20 21:48 1.6M all_mrna.sql 2020-08-20 21:48 2.1K all_est.txt.gz 2016-06-05 09:04 64M all_est.sql 2016-06-05 09:04 2.1K