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 - gc5BaseBw.txt.gz 2011-11-02 17:56 63 bigFiles.txt.gz 2024-12-01 03:27 68 extFile.txt.gz 2011-11-02 17:29 79 grp.txt.gz 2014-03-02 04:18 208 hgFindSpec.txt.gz 2023-03-28 13:54 1.0K history.txt.gz 2011-11-02 17:16 1.0K gc5BaseBw.sql 2011-11-02 17:56 1.2K ucscToEnsembl.sql 2011-11-02 17:56 1.3K chromInfo.sql 2011-11-02 16:50 1.3K ensPep.sql 2019-02-10 03:42 1.3K grp.sql 2014-03-02 04:18 1.3K extFile.sql 2011-11-02 17:29 1.4K ensemblSource.sql 2019-02-10 03:42 1.4K bigFiles.sql 2024-12-01 03:27 1.4K ensemblToGeneName.sql 2019-02-10 03:42 1.4K windowmaskerSdust.sql 2011-11-02 18:02 1.4K microsat.sql 2011-11-02 17:05 1.4K ensGtp.sql 2019-02-10 03:42 1.4K chromAlias.sql 2018-08-05 09:41 1.4K tableDescriptions.sql 2024-11-30 02:04 1.4K multiz9way.sql 2011-12-11 14:37 1.5K chainRn4Link.sql 2011-11-02 17:56 1.5K ctgPos2.sql 2011-11-02 17:16 1.5K chainHg19Link.sql 2011-11-02 17:06 1.5K chainAnoCar2Link.sql 2011-11-02 16:52 1.5K chainDanRer7Link.sql 2011-11-02 17:16 1.5K chainGalGal3Link.sql 2011-11-02 17:33 1.5K chainMelGal1Link.sql 2011-11-02 16:51 1.5K chainMonDom5Link.sql 2011-11-02 17:41 1.5K phastConsElements9way.sql 2011-12-11 14:36 1.5K genscanSubopt.sql 2011-11-02 18:03 1.5K history.sql 2011-11-02 17:16 1.5K multiz9waySummary.sql 2011-12-11 14:37 1.5K cytoBandIdeo.sql 2013-04-28 22:43 1.5K gap.sql 2011-11-02 17:05 1.5K chainMm10Link.sql 2013-10-27 22:20 1.5K tableList.sql 2024-12-01 03:27 1.6K gold.sql 2011-11-02 17:06 1.6K gbLoaded.sql 2020-09-03 10:12 1.6K genscan.sql 2011-11-02 17:15 1.6K cpgIslandExt.sql 2011-11-02 16:50 1.6K chainRn4.sql 2011-11-02 18:03 1.6K chainHg19.sql 2011-11-02 17:54 1.6K chainAnoCar2.sql 2011-11-02 17:53 1.6K chainDanRer7.sql 2011-11-02 17:30 1.6K chainGalGal3.sql 2011-11-02 17:54 1.6K chainMelGal1.sql 2011-11-02 17:29 1.6K chainMonDom5.sql 2011-11-02 18:00 1.6K multiz9wayFrames.sql 2011-12-11 14:36 1.7K tRNAs.sql 2012-04-16 05:38 1.7K phyloP9way.sql 2011-12-11 14:36 1.7K phastCons9way.sql 2011-12-11 14:36 1.7K chainMm10.sql 2013-10-27 22:20 1.7K cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K refFlat.sql 2020-09-03 10:12 1.7K hgFindSpec.sql 2023-03-28 13:54 1.8K estOrientInfo.sql 2016-05-15 11:46 1.8K rmsk.sql 2011-11-02 17:29 1.8K mrnaOrientInfo.sql 2020-09-03 10:12 1.8K simpleRepeat.sql 2011-11-02 16:50 1.9K nestedRepeats.sql 2011-11-02 17:54 1.9K ensGene.sql 2019-02-10 03:42 1.9K mgcGenes.sql 2020-03-01 09:24 1.9K augustusGene.sql 2015-07-26 17:28 1.9K refGene.sql 2020-09-03 10:12 1.9K netRn4.sql 2011-11-02 17:54 2.0K netHg19.sql 2011-11-02 17:05 2.0K netAnoCar2.sql 2011-11-02 17:53 2.0K netDanRer7.sql 2011-11-02 17:34 2.0K netGalGal3.sql 2011-11-02 17:54 2.0K netMelGal1.sql 2011-11-02 17:16 2.0K netMonDom5.sql 2011-11-02 18:02 2.0K blastHg18KG.sql 2011-11-02 17:16 2.1K trackDb.sql 2023-03-28 13:54 2.1K netMm10.sql 2013-10-27 22:20 2.1K all_est.sql 2016-05-15 11:46 2.1K intronEst.sql 2016-05-15 11:46 2.1K mgcFullMrna.sql 2020-03-01 09:24 2.1K all_mrna.sql 2020-05-11 17:36 2.1K refSeqAli.sql 2020-09-03 10:12 2.1K tableList.txt.gz 2024-12-01 03:27 4.1K tableDescriptions.txt.gz 2024-11-30 02:04 6.9K trackDb.txt.gz 2023-03-28 13:54 39K tRNAs.txt.gz 2012-04-16 05:38 56K gbLoaded.txt.gz 2020-09-03 10:12 69K ensemblSource.txt.gz 2019-02-10 03:42 73K chromAlias.txt.gz 2018-08-05 09:41 92K cytoBandIdeo.txt.gz 2013-04-28 22:43 93K chromInfo.txt.gz 2011-11-02 16:50 94K ucscToEnsembl.txt.gz 2011-11-02 17:56 97K microsat.txt.gz 2011-11-02 17:05 136K ensemblToGeneName.txt.gz 2019-02-10 03:42 140K ctgPos2.txt.gz 2011-11-02 17:16 186K ensGtp.txt.gz 2019-02-10 03:42 234K cpgIslandExt.txt.gz 2011-11-02 16:50 316K mrnaOrientInfo.txt.gz 2020-09-03 10:12 514K mgcGenes.txt.gz 2020-03-01 09:24 764K refFlat.txt.gz 2020-09-03 10:12 803K cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 854K refGene.txt.gz 2020-09-03 10:12 879K refSeqAli.txt.gz 2020-09-03 10:12 942K mgcFullMrna.txt.gz 2020-03-01 09:24 971K all_mrna.txt.gz 2020-05-11 17:36 1.9M gap.txt.gz 2011-11-02 17:05 2.0M ensGene.txt.gz 2019-02-10 03:42 2.1M augustusGene.txt.gz 2015-07-26 17:28 2.3M genscan.txt.gz 2011-11-02 17:15 2.6M blastHg18KG.txt.gz 2011-11-02 17:16 2.7M gold.txt.gz 2011-11-02 17:06 2.8M nestedRepeats.txt.gz 2011-11-02 17:54 2.9M chainMelGal1.txt.gz 2011-11-02 17:29 4.0M genscanSubopt.txt.gz 2011-11-02 18:03 4.3M netMelGal1.txt.gz 2011-11-02 17:16 5.7M multiz9waySummary.txt.gz 2011-12-11 14:37 6.1M netGalGal3.txt.gz 2011-11-02 17:54 6.3M ensPep.txt.gz 2019-02-10 03:42 6.6M netRn4.txt.gz 2011-11-02 17:54 7.2M netMonDom5.txt.gz 2011-11-02 18:02 7.3M phastConsElements9way.txt.gz 2011-12-11 14:36 8.1M netAnoCar2.txt.gz 2011-11-02 17:53 8.4M netMm10.txt.gz 2013-10-27 22:20 9.2M netHg19.txt.gz 2011-11-02 17:05 9.2M netDanRer7.txt.gz 2011-11-02 17:34 9.7M phastCons9way.txt.gz 2011-12-11 14:36 14M phyloP9way.txt.gz 2011-12-11 14:36 14M estOrientInfo.txt.gz 2016-05-15 11:46 14M chainGalGal3.txt.gz 2011-11-02 17:54 17M simpleRepeat.txt.gz 2011-11-02 16:50 19M multiz9wayFrames.txt.gz 2011-12-11 14:36 20M chainMelGal1Link.txt.gz 2011-11-02 16:52 26M intronEst.txt.gz 2016-05-15 11:46 32M multiz9way.txt.gz 2011-12-11 14:37 37M rmsk.txt.gz 2011-11-02 17:29 43M chainRn4.txt.gz 2011-11-02 18:03 44M windowmaskerSdust.txt.gz 2011-11-02 18:03 45M all_est.txt.gz 2016-05-15 11:46 53M chainMm10.txt.gz 2013-10-27 22:20 55M chainAnoCar2.txt.gz 2011-11-02 17:53 64M chainGalGal3Link.txt.gz 2011-11-02 17:33 79M chainHg19.txt.gz 2011-11-02 17:55 124M chainMonDom5.txt.gz 2011-11-02 18:01 218M chainDanRer7.txt.gz 2011-11-02 17:31 223M chainRn4Link.txt.gz 2011-11-02 17:57 285M chainMm10Link.txt.gz 2013-10-27 22:21 370M chainHg19Link.txt.gz 2011-11-02 17:08 482M chainDanRer7Link.txt.gz 2011-11-02 17:19 665M chainAnoCar2Link.txt.gz 2011-11-02 16:56 685M chainMonDom5Link.txt.gz 2011-11-02 17:44 769M