This directory contains a dump of the UCSC genome annotation database for the Sep. 2011 (Broad CanFam3.1/canFam3) assembly of the dog genome (canFam3, Broad CanFam3.1 (GCA_000002285.2)). The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: http://www.ncbi.nlm.nih.gov/genome/85 http://www.ncbi.nlm.nih.gov/genome/assembly/317138 http://www.ncbi.nlm.nih.gov/bioproject/13179 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=canFam3 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/canFam3/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/canFam3/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam3/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 canFam3 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql canFam3 --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. The dog genome sequence is made freely available by the Dog Genome Sequencing Project. Please cite the following publication when using these data: Lindblad-Toh K, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005 Dec 8;438:803-19. ------------------------------------------------------------------
Name Last modified Size Description
Parent Directory - gc5BaseBw.txt.gz 2012-06-20 14:38 63 ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 bigFiles.txt.gz 2024-12-01 03:32 94 grp.txt.gz 2014-03-02 03:40 208 history.txt.gz 2012-06-20 14:42 409 gc5BaseBw.sql 2012-06-20 14:38 1.2K ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K chromInfo.sql 2012-06-20 14:39 1.3K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K ensPep.sql 2021-05-25 14:24 1.3K grp.sql 2014-03-02 03:40 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ensemblSource.sql 2021-05-25 14:23 1.4K oregannoAttr.sql 2016-05-15 07:58 1.4K bigFiles.sql 2024-12-01 03:32 1.4K ensemblToGeneName.sql 2021-05-25 14:22 1.4K oregannoLink.sql 2016-05-15 07:58 1.4K chromAlias.sql 2018-02-18 05:41 1.4K ucscToINSDC.sql 2013-09-15 09:50 1.4K ucscToRefSeq.sql 2018-02-18 05:41 1.4K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K ensGtp.sql 2021-05-25 14:22 1.4K windowmaskerSdust.sql 2012-06-20 14:52 1.4K tableDescriptions.sql 2024-11-30 02:03 1.5K chainMm10Link.sql 2012-06-20 14:43 1.5K microsat.sql 2015-08-23 11:48 1.5K genscanSubopt.sql 2012-06-20 14:29 1.5K history.sql 2012-06-20 14:42 1.5K cytoBandIdeo.sql 2013-04-28 11:34 1.5K oreganno.sql 2016-05-15 07:58 1.5K gap.sql 2012-06-20 14:42 1.5K chainRn6Link.sql 2017-03-26 16:28 1.5K chainHg38Link.sql 2015-05-17 20:38 1.5K chainHg19Link.sql 2013-02-03 11:30 1.5K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K chainFelCat8Link.sql 2016-01-12 13:27 1.5K chainTarSyr2Link.sql 2015-05-24 21:35 1.5K chainXenTro9Link.sql 2017-12-14 09:10 1.5K chainCanFam4Link.sql 2020-05-13 01:05 1.6K tableList.sql 2024-12-01 03:32 1.6K gold.sql 2012-06-20 14:39 1.6K gbLoaded.sql 2020-08-21 01:34 1.6K genscan.sql 2012-06-20 14:42 1.6K cpgIslandExt.sql 2012-06-20 15:18 1.6K chainMm10.sql 2012-06-20 14:18 1.6K chainRn6.sql 2017-03-26 16:25 1.7K chainHg38.sql 2015-05-17 20:35 1.7K chainHg19.sql 2013-02-03 11:29 1.7K chainFelCat8.sql 2016-01-12 13:27 1.7K chainTarSyr2.sql 2015-05-24 21:34 1.7K chainXenTro9.sql 2017-12-14 09:09 1.7K cpgIslandExtUnmasked.sql 2014-06-01 09:45 1.7K refFlat.sql 2020-08-21 01:34 1.7K chainCanFam4.sql 2020-05-12 23:53 1.7K xenoRefFlat.sql 2020-08-21 01:34 1.7K estOrientInfo.sql 2016-06-12 06:28 1.8K hgFindSpec.sql 2024-07-25 09:34 1.8K rmsk.sql 2012-06-20 14:39 1.8K mrnaOrientInfo.sql 2020-08-21 01:34 1.8K simpleRepeat.sql 2012-06-20 14:42 1.9K nestedRepeats.sql 2012-06-20 14:39 1.9K geneid.sql 2015-11-22 13:35 1.9K ncbiRefSeq.sql 2020-05-10 03:26 1.9K augustusGene.sql 2015-07-26 11:03 1.9K ensGene.sql 2021-05-25 14:22 1.9K refGene.sql 2020-08-21 01:34 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K xenoRefGene.sql 2020-08-21 01:34 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K netMm10.sql 2012-06-20 14:41 2.0K trackDb.sql 2024-07-25 09:34 2.1K netRn6.sql 2017-03-26 16:50 2.1K netHg38.sql 2015-05-17 20:36 2.1K netHg19.sql 2013-02-03 11:35 2.1K netFelCat8.sql 2016-01-12 13:31 2.1K netTarSyr2.sql 2015-05-24 21:40 2.1K netXenTro9.sql 2017-12-14 09:10 2.1K all_est.sql 2016-06-12 06:24 2.1K intronEst.sql 2016-06-12 06:24 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K netCanFam4.sql 2020-05-13 01:06 2.1K all_mrna.sql 2020-08-21 00:52 2.1K xenoMrna.sql 2020-08-21 00:52 2.1K refSeqAli.sql 2020-08-21 01:34 2.1K xenoRefSeqAli.sql 2020-08-21 01:34 2.1K tableList.txt.gz 2024-12-01 03:32 4.4K tableDescriptions.txt.gz 2024-11-30 02:03 7.0K cytoBandIdeo.txt.gz 2013-04-28 11:34 18K chromInfo.txt.gz 2012-06-20 14:39 19K ucscToINSDC.txt.gz 2013-09-15 09:50 27K ucscToRefSeq.txt.gz 2018-02-18 05:41 28K chromAlias.txt.gz 2018-02-18 05:41 34K trackDb.txt.gz 2024-07-25 09:34 82K mrnaOrientInfo.txt.gz 2020-08-21 01:34 91K gbLoaded.txt.gz 2020-08-21 01:34 92K gold.txt.gz 2012-06-20 14:39 105K refFlat.txt.gz 2020-08-21 01:34 170K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 177K refGene.txt.gz 2020-08-21 01:34 182K ensemblSource.txt.gz 2021-05-25 14:23 186K refSeqAli.txt.gz 2020-08-21 01:34 187K all_mrna.txt.gz 2020-08-21 00:52 233K ensemblToGeneName.txt.gz 2021-05-25 14:22 269K gap.txt.gz 2012-06-20 14:42 330K oregannoAttr.txt.gz 2016-05-15 07:58 365K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 401K oreganno.txt.gz 2016-05-15 07:58 426K oregannoLink.txt.gz 2016-05-15 07:58 450K ensGtp.txt.gz 2021-05-25 14:22 599K microsat.txt.gz 2015-08-23 11:48 629K cpgIslandExt.txt.gz 2012-06-20 15:18 1.0M cpgIslandExtUnmasked.txt.gz 2014-06-01 09:45 1.1M seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.2M ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.1M geneid.txt.gz 2015-11-22 13:35 2.1M augustusGene.txt.gz 2015-07-26 11:04 2.3M genscan.txt.gz 2012-06-20 14:42 3.0M ensGene.txt.gz 2021-05-25 14:22 3.4M netCanFam4.txt.gz 2020-05-13 01:06 3.4M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeq.txt.gz 2020-05-10 03:26 4.0M estOrientInfo.txt.gz 2016-06-12 06:28 4.4M genscanSubopt.txt.gz 2012-06-20 14:29 5.3M ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M netXenTro9.txt.gz 2017-12-14 09:10 5.8M intronEst.txt.gz 2016-06-12 06:24 9.2M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 12M nestedRepeats.txt.gz 2012-06-20 14:39 14M ensPep.txt.gz 2021-05-25 14:24 16M all_est.txt.gz 2016-06-12 06:24 17M simpleRepeat.txt.gz 2012-06-20 14:42 23M xenoRefFlat.txt.gz 2020-08-21 01:34 28M xenoRefGene.txt.gz 2020-08-21 01:34 30M xenoRefSeqAli.txt.gz 2020-08-21 01:34 31M chainXenTro9.txt.gz 2017-12-14 09:09 46M netFelCat8.txt.gz 2016-01-12 13:31 53M chainMm10.txt.gz 2012-06-20 14:19 56M netRn6.txt.gz 2017-03-26 16:52 59M netMm10.txt.gz 2012-06-20 14:41 59M chainRn6.txt.gz 2017-03-26 16:25 60M netHg19.txt.gz 2013-02-03 11:35 64M netHg38.txt.gz 2015-05-17 20:36 64M netTarSyr2.txt.gz 2015-05-24 21:40 74M chainFelCat8.txt.gz 2016-01-12 13:27 106M rmsk.txt.gz 2012-06-20 14:40 121M windowmaskerSdust.txt.gz 2012-06-20 14:52 124M chainXenTro9Link.txt.gz 2017-12-14 09:10 181M chainHg19.txt.gz 2013-02-03 11:30 181M chainHg38.txt.gz 2015-05-17 20:35 188M xenoMrna.txt.gz 2020-08-21 00:52 270M chainTarSyr2.txt.gz 2015-05-24 21:34 298M chainMm10Link.txt.gz 2012-06-20 14:44 455M chainRn6Link.txt.gz 2017-03-26 16:33 488M chainFelCat8Link.txt.gz 2016-01-12 13:28 659M chainCanFam4.txt.gz 2020-05-12 23:53 740M chainHg19Link.txt.gz 2013-02-03 11:32 823M chainHg38Link.txt.gz 2015-05-17 20:39 857M chainTarSyr2Link.txt.gz 2015-05-24 21:36 1.1G chainCanFam4Link.txt.gz 2020-05-13 01:05 6.4G