This directory contains a dump of the UCSC genome annotation database for Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly of the pig genome (susScr2, SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2)), The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the Swine Genome Sequencing Consortium and Wellcome Trust Sange Institute. For more information on the pig genome, see the project website: http://piggenome.org/ http://www.sanger.ac.uk/resources/ 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=susScr2 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/susScr2/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/susScr2/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/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 susScr2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql susScr2 --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 - chromInfo.sql 2010-05-11 16:22 1.3K chromInfo.txt.gz 2010-05-11 16:22 219 cpgIslandExt.sql 2010-05-11 16:43 1.6K cpgIslandExt.txt.gz 2010-05-11 16:43 805K simpleRepeat.sql 2010-05-11 16:44 1.9K simpleRepeat.txt.gz 2010-05-11 16:44 14M rmsk.sql 2010-05-11 16:44 1.8K rmsk.txt.gz 2010-05-11 16:44 108M history.sql 2010-05-11 16:45 1.5K history.txt.gz 2010-05-11 16:45 567 nscanGene.sql 2010-05-11 16:46 1.9K nscanGene.txt.gz 2010-05-11 16:46 1.9M netHg19.sql 2010-05-11 16:46 2.0K netHg19.txt.gz 2010-05-11 16:46 59M netMm9.sql 2010-05-11 16:46 2.0K netMm9.txt.gz 2010-05-11 16:46 51M chainHg19Link.sql 2010-05-11 16:47 1.5K chainHg19Link.txt.gz 2010-05-11 16:48 654M gc5Base.sql 2010-05-11 16:51 1.7K gc5Base.txt.gz 2010-05-11 16:51 9.4M gold.sql 2010-05-11 16:52 1.6K gold.txt.gz 2010-05-11 16:52 2.1M chainMm9Link.sql 2010-05-11 16:52 1.5K chainMm9Link.txt.gz 2010-05-11 16:52 419M gap.sql 2010-05-11 16:55 1.5K gap.txt.gz 2010-05-11 16:55 2.1M chainMonDom5Link.sql 2010-05-11 16:55 1.5K chainMonDom5Link.txt.gz 2010-05-11 16:56 510M nestedRepeats.sql 2010-05-11 16:59 1.9K nestedRepeats.txt.gz 2010-05-11 16:59 11M ctgPos2.sql 2010-05-11 16:59 1.5K ctgPos2.txt.gz 2010-05-11 16:59 53K chainMonDom5.sql 2010-05-11 16:59 1.6K chainMonDom5.txt.gz 2010-05-11 16:59 152M chainMm9.sql 2010-05-11 17:00 1.6K chainMm9.txt.gz 2010-05-11 17:00 48M blastHg18KG.sql 2010-05-11 17:01 2.1K blastHg18KG.txt.gz 2010-05-11 17:01 3.7M chainHg19.sql 2010-05-11 17:01 1.6K chainHg19.txt.gz 2010-05-11 17:01 118M netMonDom5.sql 2010-05-11 17:01 2.0K netMonDom5.txt.gz 2010-05-11 17:01 16M ensPep.sql 2011-10-04 16:28 1.3K ensPep.txt.gz 2011-10-04 16:28 4.4M ensGtp.sql 2011-10-04 16:28 1.4K ensGtp.txt.gz 2011-10-04 16:28 167K ensGene.sql 2011-10-04 16:28 1.9K ensGene.txt.gz 2011-10-04 16:28 1.7M ensemblSource.sql 2011-10-04 16:31 1.3K ensemblSource.txt.gz 2011-10-04 16:31 62K ensemblToGeneName.sql 2011-10-04 16:31 1.3K ensemblToGeneName.txt.gz 2011-10-04 16:31 118K tRNAs.sql 2012-04-23 11:59 1.7K tRNAs.txt.gz 2012-04-23 11:59 19K chainBosTau7.sql 2012-06-17 22:40 1.6K chainBosTau7.txt.gz 2012-06-17 22:45 786M chainBosTau7Link.sql 2012-06-17 22:58 1.5K chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G netBosTau7.sql 2012-06-18 00:03 2.0K netBosTau7.txt.gz 2012-06-18 00:04 69M bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84 numtS.sql 2013-07-28 06:10 1.7K numtS.txt.gz 2013-07-28 06:10 8.7K numtSAssembled.sql 2013-07-28 06:10 1.8K numtSAssembled.txt.gz 2013-07-28 06:10 2.1K numtSMitochondrion.sql 2013-07-28 06:10 1.6K numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.0M microsat.sql 2015-08-24 02:07 1.5K microsat.txt.gz 2015-08-24 02:07 375K chr5_intronEst.sql 2016-07-17 11:25 2.1K chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M chr18_est.sql 2016-07-17 11:25 2.1K chr18_est.txt.gz 2016-07-17 11:25 1.0M chr5_est.sql 2016-07-17 11:27 2.1K chr5_est.txt.gz 2016-07-17 11:27 3.2M chr1_est.sql 2016-07-17 11:27 2.1K chr1_est.txt.gz 2016-07-17 11:27 5.2M chr11_est.sql 2016-07-17 11:27 2.1K chr11_est.txt.gz 2016-07-17 11:27 879K chr4_intronEst.sql 2016-07-17 11:27 2.1K chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M chr13_est.sql 2016-07-17 11:27 2.1K chr13_est.txt.gz 2016-07-17 11:27 2.4M chr15_est.sql 2016-07-17 11:27 2.1K chr15_est.txt.gz 2016-07-17 11:27 2.2M chr7_intronEst.sql 2016-07-17 11:27 2.1K chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M chr6_est.sql 2016-07-17 11:27 2.1K chr6_est.txt.gz 2016-07-17 11:27 3.5M chr16_est.sql 2016-07-17 11:27 2.1K chr16_est.txt.gz 2016-07-17 11:27 936K chr6_intronEst.sql 2016-07-17 11:27 2.1K chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M chr7_est.sql 2016-07-17 11:27 2.1K chr7_est.txt.gz 2016-07-17 11:27 4.0M chrX_est.sql 2016-07-17 11:27 2.1K chrX_est.txt.gz 2016-07-17 11:27 1.7M estOrientInfo.sql 2016-07-17 11:27 1.8K estOrientInfo.txt.gz 2016-07-17 11:27 16M chr9_est.sql 2016-07-17 11:27 2.1K chr9_est.txt.gz 2016-07-17 11:27 2.6M chr8_est.sql 2016-07-17 11:27 2.1K chr8_est.txt.gz 2016-07-17 11:27 2.0M chr9_intronEst.sql 2016-07-17 11:27 2.1K chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M chrX_intronEst.sql 2016-07-17 11:27 2.1K chrX_intronEst.txt.gz 2016-07-17 11:27 855K chr4_est.sql 2016-07-17 11:27 2.1K chr4_est.txt.gz 2016-07-17 11:27 3.7M chr18_intronEst.sql 2016-07-17 11:27 2.1K chr18_intronEst.txt.gz 2016-07-17 11:27 466K chr3_est.sql 2016-07-17 11:27 2.1K chr3_est.txt.gz 2016-07-17 11:27 3.2M chr3_intronEst.sql 2016-07-17 11:27 2.1K chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M chr14_est.sql 2016-07-17 11:27 2.1K chr14_est.txt.gz 2016-07-17 11:27 3.5M chr2_intronEst.sql 2016-07-17 11:27 2.1K chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M chrM_est.sql 2016-07-17 11:27 2.1K chrM_est.txt.gz 2016-07-17 11:27 1.1M chrM_mrna.sql 2016-07-17 11:27 2.1K chrM_mrna.txt.gz 2016-07-17 11:27 2.9K chr10_est.sql 2016-07-17 11:27 2.1K chr10_est.txt.gz 2016-07-17 11:27 1.1M chr13_intronEst.sql 2016-07-17 11:27 2.1K chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M chr8_intronEst.sql 2016-07-17 11:28 2.1K chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M chr17_intronEst.sql 2016-07-17 11:28 2.1K chr17_intronEst.txt.gz 2016-07-17 11:28 950K chrM_intronEst.sql 2016-07-17 11:28 2.1K chrM_intronEst.txt.gz 2016-07-17 11:28 495 chr12_est.sql 2016-07-17 11:28 2.1K chr12_est.txt.gz 2016-07-17 11:28 2.3M all_est.sql 2016-07-17 11:28 2.1K all_est.txt.gz 2016-07-17 11:28 50M chr14_intronEst.sql 2016-07-17 11:28 2.1K chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M chr1_intronEst.sql 2016-07-17 11:28 2.1K chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M chr17_est.sql 2016-07-17 11:28 2.1K chr17_est.txt.gz 2016-07-17 11:28 1.6M chr2_est.sql 2016-07-17 11:28 2.1K chr2_est.txt.gz 2016-07-17 11:28 4.1M chr11_intronEst.sql 2016-07-17 11:28 2.1K chr11_intronEst.txt.gz 2016-07-17 11:28 379K chr10_intronEst.sql 2016-07-17 11:28 2.1K chr10_intronEst.txt.gz 2016-07-17 11:28 529K chr12_intronEst.sql 2016-07-17 11:28 2.1K chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M chr15_intronEst.sql 2016-07-17 11:28 2.1K chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M chr16_intronEst.sql 2016-07-17 11:28 2.1K chr16_intronEst.txt.gz 2016-07-17 11:28 380K chr10_mrna.sql 2020-05-11 17:13 2.1K chr10_mrna.txt.gz 2020-05-11 17:13 60K chr11_mrna.sql 2020-05-11 17:13 2.1K chr11_mrna.txt.gz 2020-05-11 17:13 40K chr16_mrna.sql 2020-05-11 17:36 2.1K chr16_mrna.txt.gz 2020-05-11 17:36 50K chr3_mrna.sql 2020-05-11 17:36 2.1K chr3_mrna.txt.gz 2020-05-11 17:36 141K chrX_mrna.sql 2020-05-11 17:36 2.1K chrX_mrna.txt.gz 2020-05-11 17:36 74K chr18_mrna.sql 2020-05-11 17:36 2.1K chr18_mrna.txt.gz 2020-05-11 17:36 62K chr6_mrna.sql 2020-05-11 17:36 2.1K chr6_mrna.txt.gz 2020-05-11 17:36 168K chr12_mrna.sql 2020-05-11 17:36 2.1K chr12_mrna.txt.gz 2020-05-11 17:36 118K chr15_mrna.sql 2020-05-11 17:36 2.1K chr15_mrna.txt.gz 2020-05-11 17:36 103K chr2_mrna.sql 2020-05-11 17:36 2.1K chr2_mrna.txt.gz 2020-05-11 17:36 197K chr17_mrna.sql 2020-05-11 17:36 2.1K chr17_mrna.txt.gz 2020-05-11 17:36 82K chr9_mrna.sql 2020-05-11 17:36 2.1K chr9_mrna.txt.gz 2020-05-11 17:36 119K chr5_mrna.sql 2020-05-11 17:36 2.1K chr5_mrna.txt.gz 2020-05-11 17:36 132K chr8_mrna.sql 2020-05-11 17:36 2.1K chr8_mrna.txt.gz 2020-05-11 17:36 85K chr14_mrna.sql 2020-05-11 17:36 2.1K chr14_mrna.txt.gz 2020-05-11 17:36 158K chr13_mrna.sql 2020-09-02 07:33 2.1K chr13_mrna.txt.gz 2020-09-02 07:33 122K chr1_mrna.sql 2020-09-02 07:33 2.1K chr1_mrna.txt.gz 2020-09-02 07:33 224K chr4_mrna.sql 2020-09-02 07:33 2.1K chr4_mrna.txt.gz 2020-09-02 07:33 149K chr7_mrna.sql 2020-09-02 07:33 2.1K chr7_mrna.txt.gz 2020-09-02 07:33 245K all_mrna.sql 2020-09-02 07:33 2.1K all_mrna.txt.gz 2020-09-02 07:33 2.3M xenoMrna.sql 2020-09-02 07:33 2.1K xenoMrna.txt.gz 2020-09-02 07:33 336M mrnaOrientInfo.sql 2020-09-02 07:33 1.8K mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K xenoRefGene.sql 2020-09-02 07:33 2.0K xenoRefGene.txt.gz 2020-09-02 07:33 37M xenoRefFlat.sql 2020-09-02 07:33 1.7K xenoRefFlat.txt.gz 2020-09-02 07:33 33M xenoRefSeqAli.sql 2020-09-02 07:33 2.1K xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M gbLoaded.sql 2020-09-02 07:33 1.6K gbLoaded.txt.gz 2020-09-02 07:33 41K trackDb.sql 2023-03-28 13:53 2.1K trackDb.txt.gz 2023-03-28 13:53 36K hgFindSpec.sql 2023-03-28 13:53 1.8K hgFindSpec.txt.gz 2023-03-28 13:53 1.0K tableDescriptions.sql 2024-11-09 02:03 1.5K tableDescriptions.txt.gz 2024-11-09 02:03 5.9K tableList.sql 2024-11-10 03:06 1.6K tableList.txt.gz 2024-11-10 03:06 6.7K bigFiles.sql 2024-11-10 03:06 1.4K bigFiles.txt.gz 2024-11-10 03:06 87