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 - xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M xenoRefSeqAli.sql 2020-09-02 07:33 2.1K xenoRefGene.txt.gz 2020-09-02 07:33 37M xenoRefGene.sql 2020-09-02 07:33 2.0K xenoRefFlat.txt.gz 2020-09-02 07:33 33M xenoRefFlat.sql 2020-09-02 07:33 1.7K xenoMrna.txt.gz 2020-09-02 07:33 336M xenoMrna.sql 2020-09-02 07:33 2.1K trackDb.txt.gz 2023-03-28 13:53 36K trackDb.sql 2023-03-28 13:53 2.1K tableList.txt.gz 2024-10-13 03:07 6.7K tableList.sql 2024-10-13 03:07 1.6K tableDescriptions.txt.gz 2024-10-12 02:03 5.9K tableDescriptions.sql 2024-10-12 02:03 1.5K tRNAs.txt.gz 2012-04-23 11:59 19K tRNAs.sql 2012-04-23 11:59 1.7K simpleRepeat.txt.gz 2010-05-11 16:44 14M simpleRepeat.sql 2010-05-11 16:44 1.9K rmsk.txt.gz 2010-05-11 16:44 108M rmsk.sql 2010-05-11 16:44 1.8K numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K numtSMitochondrion.sql 2013-07-28 06:10 1.6K numtSAssembled.txt.gz 2013-07-28 06:10 2.1K numtSAssembled.sql 2013-07-28 06:10 1.8K numtS.txt.gz 2013-07-28 06:10 8.7K numtS.sql 2013-07-28 06:10 1.7K nscanGene.txt.gz 2010-05-11 16:46 1.9M nscanGene.sql 2010-05-11 16:46 1.9K netMonDom5.txt.gz 2010-05-11 17:01 16M netMonDom5.sql 2010-05-11 17:01 2.0K netMm9.txt.gz 2010-05-11 16:46 51M netMm9.sql 2010-05-11 16:46 2.0K netHg19.txt.gz 2010-05-11 16:46 59M netHg19.sql 2010-05-11 16:46 2.0K netBosTau7.txt.gz 2012-06-18 00:04 69M netBosTau7.sql 2012-06-18 00:03 2.0K nestedRepeats.txt.gz 2010-05-11 16:59 11M nestedRepeats.sql 2010-05-11 16:59 1.9K mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K mrnaOrientInfo.sql 2020-09-02 07:33 1.8K microsat.txt.gz 2015-08-24 02:07 375K microsat.sql 2015-08-24 02:07 1.5K history.txt.gz 2010-05-11 16:45 567 history.sql 2010-05-11 16:45 1.5K hgFindSpec.txt.gz 2023-03-28 13:53 1.0K hgFindSpec.sql 2023-03-28 13:53 1.8K grp.txt.gz 2014-03-02 04:14 208 grp.sql 2014-03-02 04:14 1.3K gold.txt.gz 2010-05-11 16:52 2.1M gold.sql 2010-05-11 16:52 1.6K gc5Base.txt.gz 2010-05-11 16:51 9.4M gc5Base.sql 2010-05-11 16:51 1.7K gbLoaded.txt.gz 2020-09-02 07:33 41K gbLoaded.sql 2020-09-02 07:33 1.6K gap.txt.gz 2010-05-11 16:55 2.1M gap.sql 2010-05-11 16:55 1.5K estOrientInfo.txt.gz 2016-07-17 11:27 16M estOrientInfo.sql 2016-07-17 11:27 1.8K ensemblToGeneName.txt.gz 2011-10-04 16:31 118K ensemblToGeneName.sql 2011-10-04 16:31 1.3K ensemblSource.txt.gz 2011-10-04 16:31 62K ensemblSource.sql 2011-10-04 16:31 1.3K ensPep.txt.gz 2011-10-04 16:28 4.4M ensPep.sql 2011-10-04 16:28 1.3K ensGtp.txt.gz 2011-10-04 16:28 167K ensGtp.sql 2011-10-04 16:28 1.4K ensGene.txt.gz 2011-10-04 16:28 1.7M ensGene.sql 2011-10-04 16:28 1.9K ctgPos2.txt.gz 2010-05-11 16:59 53K ctgPos2.sql 2010-05-11 16:59 1.5K cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K cpgIslandExt.txt.gz 2010-05-11 16:43 805K cpgIslandExt.sql 2010-05-11 16:43 1.6K chromInfo.txt.gz 2010-05-11 16:22 219 chromInfo.sql 2010-05-11 16:22 1.3K chrX_mrna.txt.gz 2020-05-11 17:36 74K chrX_mrna.sql 2020-05-11 17:36 2.1K chrX_intronEst.txt.gz 2016-07-17 11:27 855K chrX_intronEst.sql 2016-07-17 11:27 2.1K chrX_est.txt.gz 2016-07-17 11:27 1.7M chrX_est.sql 2016-07-17 11:27 2.1K chrM_mrna.txt.gz 2016-07-17 11:27 2.9K chrM_mrna.sql 2016-07-17 11:27 2.1K chrM_intronEst.txt.gz 2016-07-17 11:28 495 chrM_intronEst.sql 2016-07-17 11:28 2.1K chrM_est.txt.gz 2016-07-17 11:27 1.1M chrM_est.sql 2016-07-17 11:27 2.1K chr18_mrna.txt.gz 2020-05-11 17:36 62K chr18_mrna.sql 2020-05-11 17:36 2.1K chr18_intronEst.txt.gz 2016-07-17 11:27 466K chr18_intronEst.sql 2016-07-17 11:27 2.1K chr18_est.txt.gz 2016-07-17 11:25 1.0M chr18_est.sql 2016-07-17 11:25 2.1K chr17_mrna.txt.gz 2020-05-11 17:36 82K chr17_mrna.sql 2020-05-11 17:36 2.1K chr17_intronEst.txt.gz 2016-07-17 11:28 950K chr17_intronEst.sql 2016-07-17 11:28 2.1K chr17_est.txt.gz 2016-07-17 11:28 1.6M chr17_est.sql 2016-07-17 11:28 2.1K chr16_mrna.txt.gz 2020-05-11 17:36 50K chr16_mrna.sql 2020-05-11 17:36 2.1K chr16_intronEst.txt.gz 2016-07-17 11:28 380K chr16_intronEst.sql 2016-07-17 11:28 2.1K chr16_est.txt.gz 2016-07-17 11:27 936K chr16_est.sql 2016-07-17 11:27 2.1K chr15_mrna.txt.gz 2020-05-11 17:36 103K chr15_mrna.sql 2020-05-11 17:36 2.1K chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M chr15_intronEst.sql 2016-07-17 11:28 2.1K chr15_est.txt.gz 2016-07-17 11:27 2.2M chr15_est.sql 2016-07-17 11:27 2.1K chr14_mrna.txt.gz 2020-05-11 17:36 158K chr14_mrna.sql 2020-05-11 17:36 2.1K chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M chr14_intronEst.sql 2016-07-17 11:28 2.1K chr14_est.txt.gz 2016-07-17 11:27 3.5M chr14_est.sql 2016-07-17 11:27 2.1K chr13_mrna.txt.gz 2020-09-02 07:33 122K chr13_mrna.sql 2020-09-02 07:33 2.1K chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M chr13_intronEst.sql 2016-07-17 11:27 2.1K chr13_est.txt.gz 2016-07-17 11:27 2.4M chr13_est.sql 2016-07-17 11:27 2.1K chr12_mrna.txt.gz 2020-05-11 17:36 118K chr12_mrna.sql 2020-05-11 17:36 2.1K chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M chr12_intronEst.sql 2016-07-17 11:28 2.1K chr12_est.txt.gz 2016-07-17 11:28 2.3M chr12_est.sql 2016-07-17 11:28 2.1K chr11_mrna.txt.gz 2020-05-11 17:13 40K chr11_mrna.sql 2020-05-11 17:13 2.1K chr11_intronEst.txt.gz 2016-07-17 11:28 379K chr11_intronEst.sql 2016-07-17 11:28 2.1K chr11_est.txt.gz 2016-07-17 11:27 879K chr11_est.sql 2016-07-17 11:27 2.1K chr10_mrna.txt.gz 2020-05-11 17:13 60K chr10_mrna.sql 2020-05-11 17:13 2.1K chr10_intronEst.txt.gz 2016-07-17 11:28 529K chr10_intronEst.sql 2016-07-17 11:28 2.1K chr10_est.txt.gz 2016-07-17 11:27 1.1M chr10_est.sql 2016-07-17 11:27 2.1K chr9_mrna.txt.gz 2020-05-11 17:36 119K chr9_mrna.sql 2020-05-11 17:36 2.1K chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M chr9_intronEst.sql 2016-07-17 11:27 2.1K chr9_est.txt.gz 2016-07-17 11:27 2.6M chr9_est.sql 2016-07-17 11:27 2.1K chr8_mrna.txt.gz 2020-05-11 17:36 85K chr8_mrna.sql 2020-05-11 17:36 2.1K chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M chr8_intronEst.sql 2016-07-17 11:28 2.1K chr8_est.txt.gz 2016-07-17 11:27 2.0M chr8_est.sql 2016-07-17 11:27 2.1K chr7_mrna.txt.gz 2020-09-02 07:33 245K chr7_mrna.sql 2020-09-02 07:33 2.1K chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M chr7_intronEst.sql 2016-07-17 11:27 2.1K chr7_est.txt.gz 2016-07-17 11:27 4.0M chr7_est.sql 2016-07-17 11:27 2.1K chr6_mrna.txt.gz 2020-05-11 17:36 168K chr6_mrna.sql 2020-05-11 17:36 2.1K chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M chr6_intronEst.sql 2016-07-17 11:27 2.1K chr6_est.txt.gz 2016-07-17 11:27 3.5M chr6_est.sql 2016-07-17 11:27 2.1K chr5_mrna.txt.gz 2020-05-11 17:36 132K chr5_mrna.sql 2020-05-11 17:36 2.1K chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M chr5_intronEst.sql 2016-07-17 11:25 2.1K chr5_est.txt.gz 2016-07-17 11:27 3.2M chr5_est.sql 2016-07-17 11:27 2.1K chr4_mrna.txt.gz 2020-09-02 07:33 149K chr4_mrna.sql 2020-09-02 07:33 2.1K chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M chr4_intronEst.sql 2016-07-17 11:27 2.1K chr4_est.txt.gz 2016-07-17 11:27 3.7M chr4_est.sql 2016-07-17 11:27 2.1K chr3_mrna.txt.gz 2020-05-11 17:36 141K chr3_mrna.sql 2020-05-11 17:36 2.1K chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M chr3_intronEst.sql 2016-07-17 11:27 2.1K chr3_est.txt.gz 2016-07-17 11:27 3.2M chr3_est.sql 2016-07-17 11:27 2.1K chr2_mrna.txt.gz 2020-05-11 17:36 197K chr2_mrna.sql 2020-05-11 17:36 2.1K chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M chr2_intronEst.sql 2016-07-17 11:27 2.1K chr2_est.txt.gz 2016-07-17 11:28 4.1M chr2_est.sql 2016-07-17 11:28 2.1K chr1_mrna.txt.gz 2020-09-02 07:33 224K chr1_mrna.sql 2020-09-02 07:33 2.1K chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M chr1_intronEst.sql 2016-07-17 11:28 2.1K chr1_est.txt.gz 2016-07-17 11:27 5.2M chr1_est.sql 2016-07-17 11:27 2.1K chainMonDom5Link.txt.gz 2010-05-11 16:56 510M chainMonDom5Link.sql 2010-05-11 16:55 1.5K chainMonDom5.txt.gz 2010-05-11 16:59 152M chainMonDom5.sql 2010-05-11 16:59 1.6K chainMm9Link.txt.gz 2010-05-11 16:52 419M chainMm9Link.sql 2010-05-11 16:52 1.5K chainMm9.txt.gz 2010-05-11 17:00 48M chainMm9.sql 2010-05-11 17:00 1.6K chainHg19Link.txt.gz 2010-05-11 16:48 654M chainHg19Link.sql 2010-05-11 16:47 1.5K chainHg19.txt.gz 2010-05-11 17:01 118M chainHg19.sql 2010-05-11 17:01 1.6K chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G chainBosTau7Link.sql 2012-06-17 22:58 1.5K chainBosTau7.txt.gz 2012-06-17 22:45 786M chainBosTau7.sql 2012-06-17 22:40 1.6K blastHg18KG.txt.gz 2010-05-11 17:01 3.7M blastHg18KG.sql 2010-05-11 17:01 2.1K bigFiles.txt.gz 2024-10-13 03:07 87 bigFiles.sql 2024-10-13 03:07 1.4K bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84 bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K augustusGene.txt.gz 2015-07-26 17:28 2.0M augustusGene.sql 2015-07-26 17:28 1.9K all_mrna.txt.gz 2020-09-02 07:33 2.3M all_mrna.sql 2020-09-02 07:33 2.1K all_est.txt.gz 2016-07-17 11:28 50M all_est.sql 2016-07-17 11:28 2.1K