This directory contains a dump of the UCSC genome annotation database for the Oct. 2004 assembly of the opossum genome (UCSC version monDom1) from the Broad Institute at MIT and Harvard. The directory is updated nightly. The .txt.gz files contain the database tables in a tab-delimited format compressed with gzip. The .sql files contain the MySQL commands used to create the tables. 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=monDom1 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 that 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/monDom1/database. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) All the tables in this directory are freely usable for any purpose. The opossum sequence is made freely available before scientific publication with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing particular genes and regions if the providers of these data (The Broad Institute) are properly acknowledged. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chainHg17Link.txt.gz 2005-01-15 05:44 476M rmsk.txt.gz 2005-01-15 06:10 446M chainMm6Link.txt.gz 2005-05-05 06:43 369M xenoMrna.txt.gz 2016-02-21 20:04 290M quality.txt.gz 2005-01-15 06:04 67M chainGalGal2Link.txt.gz 2005-01-15 05:38 67M chainDanRer2Link.txt.gz 2005-01-15 05:37 46M chainHg17.txt.gz 2005-01-15 05:39 40M netHg17.txt.gz 2005-01-15 06:01 35M chainMm6.txt.gz 2005-05-05 06:37 34M xenoRefGene.txt.gz 2020-08-22 12:05 34M xenoRefSeqAli.txt.gz 2020-08-22 12:05 32M xenoRefFlat.txt.gz 2020-08-22 12:05 31M phastCons5.txt.gz 2005-01-20 04:50 30M netMm6.txt.gz 2005-05-05 06:48 22M mostConserved.txt.gz 2005-01-15 05:59 19M simpleRepeat.txt.gz 2005-01-15 06:14 16M multiz5way.txt.gz 2005-01-15 05:59 15M gc5Base.txt.gz 2005-01-15 05:58 14M hg17_netBlastz.txt.gz 2005-01-20 04:52 11M netGalGal2.txt.gz 2005-01-15 06:00 9.4M genscanPep.txt.gz 2005-01-15 05:58 8.8M chainGalGal2.txt.gz 2005-01-15 05:37 8.7M mm5_netBlastz.txt.gz 2005-01-20 04:52 7.3M netDanRer2.txt.gz 2005-01-15 06:00 6.0M chainDanRer2.txt.gz 2005-01-15 05:36 4.7M blastHg17KG.txt.gz 2005-01-15 05:36 4.3M galGal2_netBlastz.txt.gz 2005-01-20 04:51 4.2M genscan.txt.gz 2005-01-15 05:58 2.4M danRer2_netBlastz.txt.gz 2005-01-20 04:51 2.2M augustusGene.txt.gz 2015-07-26 16:38 2.0M gold.txt.gz 2005-01-15 05:59 1.8M gap.txt.gz 2005-01-15 05:57 1.1M microsat.txt.gz 2006-08-03 07:52 1.0M cpgIslandExtUnmasked.txt.gz 2014-06-01 16:52 594K contigAcc.txt.gz 2005-03-24 05:08 546K cpgIslandExt.txt.gz 2005-01-15 05:57 545K gbDelete_tmp.txt.gz 2009-08-19 15:43 171K chromInfo.txt.gz 2005-01-15 05:57 105K all_mrna.txt.gz 2019-03-17 11:24 65K trackDb.txt.gz 2023-03-28 13:51 25K gbLoaded.txt.gz 2020-08-22 12:20 15K mrnaOrientInfo.txt.gz 2019-03-17 11:24 14K tableDescriptions.txt.gz 2024-08-31 02:03 5.5K tableList.txt.gz 2024-09-01 03:25 3.0K xenoMrna.sql 2016-02-21 20:04 2.4K xenoRefSeqAli.sql 2020-08-22 12:05 2.1K all_mrna.sql 2019-03-17 11:24 2.1K trackDb.sql 2023-03-28 13:51 2.1K xenoRefGene.sql 2020-08-22 12:05 2.0K augustusGene.sql 2015-07-26 16:38 1.9K mrnaOrientInfo.sql 2019-03-17 11:24 1.8K hgFindSpec.sql 2023-03-28 13:51 1.8K xenoRefFlat.sql 2020-08-22 12:05 1.7K cpgIslandExtUnmasked.sql 2014-06-01 16:52 1.7K gbLoaded.sql 2020-08-22 12:20 1.6K tableList.sql 2024-09-01 03:25 1.6K tableDescriptions.sql 2024-08-31 02:03 1.4K bigFiles.sql 2024-09-01 03:25 1.4K grp.sql 2014-03-02 04:14 1.4K blastHg17KG.sql 2013-10-01 12:48 1.3K netGalGal2.sql 2013-10-01 12:48 1.3K netDanRer2.sql 2013-10-01 12:48 1.3K netHg17.sql 2013-10-01 12:48 1.3K netMm6.sql 2013-10-01 12:48 1.3K microsat.sql 2006-08-03 07:52 1.3K gbDelete_tmp.sql 2009-08-19 15:43 1.3K simpleRepeat.sql 2013-10-01 12:48 1.1K rmsk.sql 2013-10-01 12:48 1.1K phastCons5.sql 2013-10-01 12:48 898 quality.sql 2013-10-01 12:48 890 gc5Base.sql 2013-10-01 12:48 890 chainGalGal2.sql 2013-10-01 12:48 886 chainDanRer2.sql 2013-10-01 12:48 886 chainHg17.sql 2013-10-01 12:48 880 chainMm6.sql 2013-10-01 12:48 878 gold.sql 2013-10-01 12:48 799 cpgIslandExt.sql 2013-10-01 12:48 751 genscan.sql 2013-10-01 12:48 748 hgFindSpec.txt.gz 2023-03-28 13:51 732 gap.sql 2013-10-01 12:48 722 galGal2_netBlastz.sql 2013-10-01 12:48 675 danRer2_netBlastz.sql 2013-10-01 12:48 675 hg17_netBlastz.sql 2013-10-01 12:48 669 mm5_netBlastz.sql 2013-10-01 12:48 667 multiz5way.sql 2013-10-01 12:48 661 mostConserved.sql 2013-10-01 12:48 650 chainGalGal2Link.sql 2013-10-01 12:48 585 chainDanRer2Link.sql 2013-10-01 12:48 585 chainHg17Link.sql 2013-10-01 12:48 579 chainMm6Link.sql 2013-10-01 12:48 577 history.sql 2013-10-01 12:48 537 history.txt.gz 2005-01-15 05:59 508 extFile.sql 2013-10-01 12:48 445 chromInfo.sql 2013-10-01 12:48 396 contigAcc.sql 2013-10-01 12:48 343 genscanPep.sql 2013-10-01 12:48 330 grp.txt.gz 2014-03-02 04:14 223 extFile.txt.gz 2005-01-15 05:57 182 bigFiles.txt.gz 2024-09-01 03:25 33