This directory contains a dump of the UCSC genome annotation database for the Nov. 2009 (JGI 4.2/xenTro3) assembly of the Xenopus (Silurana) tropicalis (western clawed frog) genome (xenTro3, US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1)) from the X. tropicalis Genome Consortium. The annotations were generated by UCSC and collaborators worldwide. This assembly was produced by the US DOE Joint Genome Institute (JGI). For more information on the X. tropicalis genome, please note the NCBI WGS Traces information: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAMC01 and the project website: http://genome.jgi-psf.org/Xentr4/Xentr4.home.html 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=xenTro3 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/xenTro3/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/xenTro3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro3/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 xenTro3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql xenTro3 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ========================================================================== Data use policy from: http://genome.jgi-psf.org/Xentr4/Xentr4.download.html Preliminary drafts of the X. tropicalis sequence are made freely available before scientific publication by the JGI and the X. tropicalis Genome Consortium, 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 provider of this data (DOE Joint Genome Institute) is properly acknowledged. 3. Additional shotgun sequencing is ongoing, and future assembly releases will be made in a timely fashion. We expect to publish an initial analysis of a high quality draft X. tropicalis genome sequence in 2005 (with submission targeted for the spring of 2005) which will include descriptions of the large scale organization of the frog genome as well as genome-scale comparisons of the frog sequence and gene set with those of other animals. Others who would like to coordinate other genome-wide analysis with this work should contact Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated approach to describing this community resource. 4. Any redistribution of the data should carry this notice. ==========================================================================
Name Last modified Size Description
Parent Directory - simpleRepeat.sql 2011-11-02 16:50 1.9K simpleRepeat.txt.gz 2011-11-02 16:50 19M cpgIslandExt.sql 2011-11-02 16:50 1.6K cpgIslandExt.txt.gz 2011-11-02 16:50 316K chromInfo.sql 2011-11-02 16:50 1.3K chromInfo.txt.gz 2011-11-02 16:50 94K chainMelGal1Link.sql 2011-11-02 16:51 1.5K chainMelGal1Link.txt.gz 2011-11-02 16:52 26M chainAnoCar2Link.sql 2011-11-02 16:52 1.5K chainAnoCar2Link.txt.gz 2011-11-02 16:56 685M gap.sql 2011-11-02 17:05 1.5K gap.txt.gz 2011-11-02 17:05 2.0M microsat.sql 2011-11-02 17:05 1.4K microsat.txt.gz 2011-11-02 17:05 136K netHg19.sql 2011-11-02 17:05 2.0K netHg19.txt.gz 2011-11-02 17:05 9.2M gold.sql 2011-11-02 17:06 1.6K gold.txt.gz 2011-11-02 17:06 2.8M chainHg19Link.sql 2011-11-02 17:06 1.5K chainHg19Link.txt.gz 2011-11-02 17:08 482M genscan.sql 2011-11-02 17:15 1.6K genscan.txt.gz 2011-11-02 17:15 2.6M history.sql 2011-11-02 17:16 1.5K history.txt.gz 2011-11-02 17:16 1.0K ctgPos2.sql 2011-11-02 17:16 1.5K ctgPos2.txt.gz 2011-11-02 17:16 186K netMelGal1.sql 2011-11-02 17:16 2.0K netMelGal1.txt.gz 2011-11-02 17:16 5.7M blastHg18KG.sql 2011-11-02 17:16 2.1K blastHg18KG.txt.gz 2011-11-02 17:16 2.7M chainDanRer7Link.sql 2011-11-02 17:16 1.5K chainDanRer7Link.txt.gz 2011-11-02 17:19 665M chainMelGal1.sql 2011-11-02 17:29 1.6K chainMelGal1.txt.gz 2011-11-02 17:29 4.0M extFile.sql 2011-11-02 17:29 1.4K extFile.txt.gz 2011-11-02 17:29 79 rmsk.sql 2011-11-02 17:29 1.8K rmsk.txt.gz 2011-11-02 17:29 43M chainDanRer7.sql 2011-11-02 17:30 1.6K chainDanRer7.txt.gz 2011-11-02 17:31 223M chainGalGal3Link.sql 2011-11-02 17:33 1.5K chainGalGal3Link.txt.gz 2011-11-02 17:33 79M netDanRer7.sql 2011-11-02 17:34 2.0K netDanRer7.txt.gz 2011-11-02 17:34 9.7M chainMonDom5Link.sql 2011-11-02 17:41 1.5K chainMonDom5Link.txt.gz 2011-11-02 17:44 769M netAnoCar2.sql 2011-11-02 17:53 2.0K netAnoCar2.txt.gz 2011-11-02 17:53 8.4M chainAnoCar2.sql 2011-11-02 17:53 1.6K chainAnoCar2.txt.gz 2011-11-02 17:53 64M nestedRepeats.sql 2011-11-02 17:54 1.9K nestedRepeats.txt.gz 2011-11-02 17:54 2.9M chainGalGal3.sql 2011-11-02 17:54 1.6K chainGalGal3.txt.gz 2011-11-02 17:54 17M netGalGal3.sql 2011-11-02 17:54 2.0K netGalGal3.txt.gz 2011-11-02 17:54 6.3M netRn4.sql 2011-11-02 17:54 2.0K netRn4.txt.gz 2011-11-02 17:54 7.2M chainHg19.sql 2011-11-02 17:54 1.6K chainHg19.txt.gz 2011-11-02 17:55 124M ucscToEnsembl.sql 2011-11-02 17:56 1.3K ucscToEnsembl.txt.gz 2011-11-02 17:56 97K gc5BaseBw.sql 2011-11-02 17:56 1.2K gc5BaseBw.txt.gz 2011-11-02 17:56 63 chainRn4Link.sql 2011-11-02 17:56 1.5K chainRn4Link.txt.gz 2011-11-02 17:57 285M chainMonDom5.sql 2011-11-02 18:00 1.6K chainMonDom5.txt.gz 2011-11-02 18:01 218M netMonDom5.sql 2011-11-02 18:02 2.0K netMonDom5.txt.gz 2011-11-02 18:02 7.3M windowmaskerSdust.sql 2011-11-02 18:02 1.4K windowmaskerSdust.txt.gz 2011-11-02 18:03 45M chainRn4.sql 2011-11-02 18:03 1.6K chainRn4.txt.gz 2011-11-02 18:03 44M genscanSubopt.sql 2011-11-02 18:03 1.5K genscanSubopt.txt.gz 2011-11-02 18:03 4.3M phastCons9way.sql 2011-12-11 14:36 1.7K phastCons9way.txt.gz 2011-12-11 14:36 14M multiz9wayFrames.sql 2011-12-11 14:36 1.7K multiz9wayFrames.txt.gz 2011-12-11 14:36 20M phyloP9way.sql 2011-12-11 14:36 1.7K phyloP9way.txt.gz 2011-12-11 14:36 14M phastConsElements9way.sql 2011-12-11 14:36 1.5K phastConsElements9way.txt.gz 2011-12-11 14:36 8.1M multiz9way.sql 2011-12-11 14:37 1.5K multiz9way.txt.gz 2011-12-11 14:37 37M multiz9waySummary.sql 2011-12-11 14:37 1.5K multiz9waySummary.txt.gz 2011-12-11 14:37 6.1M tRNAs.sql 2012-04-16 05:38 1.7K tRNAs.txt.gz 2012-04-16 05:38 56K cytoBandIdeo.sql 2013-04-28 22:43 1.5K cytoBandIdeo.txt.gz 2013-04-28 22:43 93K netMm10.sql 2013-10-27 22:20 2.1K netMm10.txt.gz 2013-10-27 22:20 9.2M chainMm10.sql 2013-10-27 22:20 1.7K chainMm10.txt.gz 2013-10-27 22:20 55M chainMm10Link.sql 2013-10-27 22:20 1.5K chainMm10Link.txt.gz 2013-10-27 22:21 370M grp.sql 2014-03-02 04:18 1.3K grp.txt.gz 2014-03-02 04:18 208 cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 854K augustusGene.sql 2015-07-26 17:28 1.9K augustusGene.txt.gz 2015-07-26 17:28 2.3M estOrientInfo.sql 2016-05-15 11:46 1.8K estOrientInfo.txt.gz 2016-05-15 11:46 14M all_est.sql 2016-05-15 11:46 2.1K all_est.txt.gz 2016-05-15 11:46 53M intronEst.sql 2016-05-15 11:46 2.1K intronEst.txt.gz 2016-05-15 11:46 32M chromAlias.sql 2018-08-05 09:41 1.4K chromAlias.txt.gz 2018-08-05 09:41 92K ensGtp.sql 2019-02-10 03:42 1.4K ensGtp.txt.gz 2019-02-10 03:42 234K ensPep.sql 2019-02-10 03:42 1.3K ensPep.txt.gz 2019-02-10 03:42 6.6M ensemblToGeneName.sql 2019-02-10 03:42 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:42 140K ensGene.sql 2019-02-10 03:42 1.9K ensGene.txt.gz 2019-02-10 03:42 2.1M ensemblSource.sql 2019-02-10 03:42 1.4K ensemblSource.txt.gz 2019-02-10 03:42 73K mgcFullMrna.sql 2020-03-01 09:24 2.1K mgcFullMrna.txt.gz 2020-03-01 09:24 971K mgcGenes.sql 2020-03-01 09:24 1.9K mgcGenes.txt.gz 2020-03-01 09:24 764K all_mrna.sql 2020-05-11 17:36 2.1K all_mrna.txt.gz 2020-05-11 17:36 1.9M gbLoaded.sql 2020-09-03 10:12 1.6K gbLoaded.txt.gz 2020-09-03 10:12 69K mrnaOrientInfo.sql 2020-09-03 10:12 1.8K mrnaOrientInfo.txt.gz 2020-09-03 10:12 514K refFlat.sql 2020-09-03 10:12 1.7K refFlat.txt.gz 2020-09-03 10:12 803K refGene.sql 2020-09-03 10:12 1.9K refGene.txt.gz 2020-09-03 10:12 879K refSeqAli.sql 2020-09-03 10:12 2.1K refSeqAli.txt.gz 2020-09-03 10:12 942K trackDb.sql 2023-03-28 13:54 2.1K trackDb.txt.gz 2023-03-28 13:54 39K hgFindSpec.sql 2023-03-28 13:54 1.8K hgFindSpec.txt.gz 2023-03-28 13:54 1.0K tableDescriptions.sql 2024-12-07 02:04 1.4K tableDescriptions.txt.gz 2024-12-07 02:04 6.9K tableList.sql 2024-12-08 03:28 1.6K tableList.txt.gz 2024-12-08 03:28 4.1K bigFiles.sql 2024-12-08 03:28 1.4K bigFiles.txt.gz 2024-12-08 03:28 68