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 - bigFiles.txt.gz 2024-12-08 03:24 33 extFile.txt.gz 2008-04-07 14:51 85 grp.txt.gz 2014-03-02 03:37 208 history.txt.gz 2008-04-07 15:10 742 hgFindSpec.txt.gz 2023-03-28 13:46 1.0K nscanPep.sql 2008-04-25 03:16 1.1K chromInfo.sql 2008-04-07 15:04 1.2K ensPep.sql 2011-03-14 08:25 1.3K extFile.sql 2008-04-07 14:51 1.3K genscanPep.sql 2010-10-31 13:25 1.3K ensemblSource.sql 2011-10-03 07:42 1.3K ensemblToGeneName.sql 2011-10-03 07:42 1.3K ensGtp.sql 2011-03-14 08:23 1.4K grp.sql 2014-03-02 03:37 1.4K bigFiles.sql 2024-12-08 03:24 1.4K chainMm9Link.sql 2008-04-07 14:20 1.4K multiz5way.sql 2008-04-07 15:16 1.4K chainCanFam2Link.sql 2008-04-07 12:20 1.4K chainOrnAna1Link.sql 2008-04-07 14:51 1.4K history.sql 2008-04-07 15:10 1.4K phastConsElements5way.sql 2008-04-07 15:36 1.4K tableDescriptions.sql 2024-12-07 02:03 1.5K multiz5waySummary.sql 2008-04-07 15:21 1.5K chainOviAri1Link.sql 2011-04-25 07:32 1.5K chainSusScr2Link.sql 2010-05-16 11:22 1.5K microsat.sql 2015-08-23 10:14 1.5K gap.sql 2008-04-07 15:04 1.5K cytoBandIdeo.sql 2013-08-11 03:45 1.5K chainHg19Link.sql 2009-09-20 07:34 1.5K genscan.sql 2008-04-07 15:10 1.6K tableList.sql 2024-12-08 03:24 1.6K gold.sql 2008-04-07 15:10 1.6K gbLoaded.sql 2020-08-20 21:54 1.6K cpgIslandExt.sql 2008-04-07 15:04 1.6K chainMm9.sql 2008-04-07 14:17 1.6K chainOviAri1.sql 2011-04-25 08:41 1.6K chainSusScr2.sql 2010-05-16 11:01 1.6K chainCanFam2.sql 2008-04-07 12:14 1.7K chainOrnAna1.sql 2008-04-07 14:49 1.7K multiz5wayFrames.sql 2008-04-07 15:21 1.7K tRNAs.sql 2012-04-22 18:28 1.7K wgEncodeNhgriBip.sql 2009-08-02 05:56 1.7K cpgIslandExtUnmasked.sql 2014-06-01 08:32 1.7K gc5Base.sql 2008-04-07 15:09 1.7K quality.sql 2008-04-07 15:36 1.7K refFlat.sql 2020-08-20 21:48 1.7K phastCons5way.sql 2008-04-07 15:31 1.7K xenoRefFlat.sql 2020-08-20 21:48 1.7K hgFindSpec.sql 2023-03-28 13:46 1.8K estOrientInfo.sql 2016-06-05 09:04 1.8K chainHg19.sql 2009-09-20 07:33 1.8K mrnaOrientInfo.sql 2020-08-20 21:48 1.8K ensGene.sql 2011-03-14 08:23 1.9K rmsk.sql 2008-04-07 15:40 1.9K nscanGene.sql 2008-04-25 03:16 1.9K nestedRepeats.sql 2008-04-07 15:21 1.9K simpleRepeat.sql 2008-04-07 15:46 1.9K mgcGenes.sql 2020-03-01 04:52 1.9K augustusGene.sql 2015-07-26 10:13 1.9K refGene.sql 2020-08-20 21:48 1.9K xenoRefGene.sql 2020-08-20 21:48 2.0K netOviAri1.sql 2011-04-25 07:31 2.0K netSusScr2.sql 2010-05-16 11:22 2.0K trackDb.sql 2023-03-28 13:46 2.1K all_est.sql 2016-06-05 09:04 2.1K xenoMrna.sql 2016-02-21 10:02 2.1K intronEst.sql 2016-06-05 09:03 2.1K mgcFullMrna.sql 2020-03-01 04:52 2.1K all_mrna.sql 2020-08-20 21:48 2.1K refSeqAli.sql 2020-08-20 21:48 2.1K xenoRefSeqAli.sql 2020-08-20 21:48 2.1K netMm9.sql 2008-04-07 15:12 2.2K netCanFam2.sql 2008-04-07 15:22 2.2K netOrnAna1.sql 2008-04-07 15:30 2.2K blastHg18KG.sql 2009-12-20 10:21 2.3K netHg19.sql 2009-09-20 07:41 2.3K tableList.txt.gz 2024-12-08 03:24 4.2K tableDescriptions.txt.gz 2024-12-07 02:03 6.8K wgEncodeNhgriBip.txt.gz 2009-08-02 05:56 11K gbLoaded.txt.gz 2020-08-20 21:54 43K trackDb.txt.gz 2023-03-28 13:46 50K cytoBandIdeo.txt.gz 2013-08-11 03:45 56K chromInfo.txt.gz 2008-04-07 15:04 60K tRNAs.txt.gz 2012-04-22 18:28 109K ensemblSource.txt.gz 2011-10-03 07:42 119K ensemblToGeneName.txt.gz 2011-10-03 07:42 199K microsat.txt.gz 2015-08-23 10:14 299K ensGtp.txt.gz 2011-03-14 08:23 323K mrnaOrientInfo.txt.gz 2020-08-20 21:48 591K mgcGenes.txt.gz 2020-03-01 04:52 803K cpgIslandExt.txt.gz 2008-04-07 15:04 805K cpgIslandExtUnmasked.txt.gz 2014-06-01 08:32 889K mgcFullMrna.txt.gz 2020-03-01 04:52 908K gap.txt.gz 2008-04-07 15:04 1.0M refFlat.txt.gz 2020-08-20 21:48 1.4M nscanGene.txt.gz 2008-04-25 03:16 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 21:48 1.6M gold.txt.gz 2008-04-07 15:10 2.3M augustusGene.txt.gz 2015-07-26 10:13 2.3M ensGene.txt.gz 2011-03-14 08:23 2.4M genscan.txt.gz 2008-04-07 15:10 3.2M blastHg18KG.txt.gz 2009-12-20 10:21 4.0M nscanPep.txt.gz 2008-04-25 03:16 5.1M ensPep.txt.gz 2011-03-14 08:25 7.3M multiz5wayFrames.txt.gz 2008-04-07 15:21 7.7M multiz5waySummary.txt.gz 2008-04-07 15:21 9.8M phastConsElements5way.txt.gz 2008-04-07 15:36 9.8M genscanPep.txt.gz 2010-10-31 13:25 11M gc5Base.txt.gz 2008-04-07 15:10 11M simpleRepeat.txt.gz 2008-04-07 15:46 12M nestedRepeats.txt.gz 2008-04-07 15:22 15M netOrnAna1.txt.gz 2008-04-07 15:31 18M estOrientInfo.txt.gz 2016-06-05 09:04 20M xenoRefFlat.txt.gz 2020-08-20 21:48 29M xenoRefSeqAli.txt.gz 2020-08-20 21:48 31M xenoRefGene.txt.gz 2020-08-20 21:48 32M intronEst.txt.gz 2016-06-05 09:03 37M chainOrnAna1.txt.gz 2008-04-07 14:50 45M netMm9.txt.gz 2008-04-07 15:15 56M quality.txt.gz 2008-04-07 15:39 58M all_est.txt.gz 2016-06-05 09:04 64M chainMm9.txt.gz 2008-04-07 14:19 64M netHg19.txt.gz 2009-09-20 07:41 68M phastCons5way.txt.gz 2008-04-07 15:34 70M netSusScr2.txt.gz 2010-05-16 11:22 73M netCanFam2.txt.gz 2008-04-07 15:25 73M chainCanFam2.txt.gz 2008-04-07 12:17 74M netOviAri1.txt.gz 2011-04-25 07:31 80M multiz5way.txt.gz 2008-04-07 15:19 91M rmsk.txt.gz 2008-04-07 15:43 135M chainHg19.txt.gz 2009-09-20 07:33 234M chainOrnAna1Link.txt.gz 2008-04-07 14:58 249M xenoMrna.txt.gz 2016-02-21 10:04 309M chainMm9Link.txt.gz 2008-04-07 14:35 497M chainCanFam2Link.txt.gz 2008-04-07 12:48 670M chainHg19Link.txt.gz 2009-09-20 07:36 968M chainOviAri1.txt.gz 2011-04-25 08:52 2.3G chainSusScr2.txt.gz 2010-05-16 11:07 3.0G chainOviAri1Link.txt.gz 2011-04-25 07:49 4.3G chainSusScr2Link.txt.gz 2010-05-16 11:47 12G