This directory contains a dump of the UCSC genome annotation database for the May 2019 (UMICH_Zoey_3.1/canFam5) assembly of the dog genome (canFam5, University of Michigan) . The annotations were generated by UCSC and collaborators worldwide. For more information about this assembly, please note the NCBI resources: https://www.ncbi.nlm.nih.gov/genome/85 https://www.ncbi.nlm.nih.gov/genome/assembly/3218611 https://www.ncbi.nlm.nih.gov/bioproject/318403 https://www.ncbi.nlm.nih.gov/biosample/SAMN04851098 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=canFam5 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.soe.ucsc.edu, then go to the directory goldenPath/canFam5/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.soe.ucsc.edu/goldenPath/canFam5/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/gc5Base.txt.gz' -O gc5Base.txt.gz 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 canFam5 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql canFam5 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' ----------------------------------------------------------------------------- GenBank Data Usage The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank. ----------------------------------------------------------------------------- All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory - gc5BaseBw.txt.gz 2020-07-17 16:00 66 crisprAllTargets.txt.gz 2020-09-14 01:39 69 bigFiles.txt.gz 2024-12-08 03:04 95 grp.txt.gz 2020-07-17 16:00 213 history.txt.gz 2020-09-14 01:39 858 hgFindSpec.txt.gz 2024-01-31 15:13 863 gc5BaseBw.sql 2020-07-17 16:00 1.3K crisprAllTargets.sql 2020-09-14 01:39 1.3K ensPep.sql 2021-05-25 14:23 1.3K gbLoaded.txt.gz 2020-08-18 12:19 1.4K grp.sql 2020-07-17 16:00 1.4K ensemblSource.sql 2021-05-25 14:23 1.4K bigFiles.sql 2024-12-08 03:04 1.4K ensemblToGeneName.sql 2021-05-25 14:22 1.4K chromInfo.sql 2020-07-17 16:00 1.4K tableDescriptions.sql 2024-12-07 02:04 1.4K ensGtp.sql 2021-05-25 14:22 1.4K chromAlias.sql 2020-07-29 13:24 1.4K ucscToINSDC.sql 2020-07-29 14:00 1.4K microsat.sql 2020-07-28 07:50 1.5K windowmaskerSdust.sql 2020-07-28 08:54 1.5K cytoBandIdeo.sql 2020-07-17 20:10 1.5K chainHg38Link.sql 2020-08-17 13:25 1.6K chainMm10Link.sql 2020-08-17 13:06 1.6K chainMm39Link.sql 2020-09-08 13:43 1.6K tableList.sql 2024-12-08 03:04 1.6K history.sql 2020-09-14 01:39 1.6K gbLoaded.sql 2020-08-18 12:19 1.6K gap.sql 2020-07-17 15:52 1.6K gold.sql 2020-07-17 15:52 1.7K genscan.sql 2020-07-31 12:18 1.7K cpgIslandExt.sql 2020-07-28 09:15 1.7K chainHg38.sql 2020-08-17 13:19 1.7K chainMm10.sql 2020-08-17 13:03 1.7K chainMm39.sql 2020-09-08 13:40 1.7K refFlat.sql 2020-08-18 06:37 1.7K cpgIslandExtUnmasked.sql 2020-07-17 16:59 1.7K xenoRefFlat.sql 2020-08-18 06:37 1.7K hgFindSpec.sql 2024-01-31 15:13 1.8K estOrientInfo.sql 2020-08-18 11:45 1.8K mrnaOrientInfo.sql 2020-08-18 12:16 1.8K rmsk.sql 2020-07-18 06:31 1.9K ensGene.sql 2021-05-25 14:22 1.9K refGene.sql 2020-08-18 06:37 1.9K simpleRepeat.sql 2020-07-17 17:05 1.9K nestedRepeats.sql 2020-07-18 06:33 2.0K xenoRefGene.sql 2020-08-18 06:37 2.0K augustusGene.sql 2020-07-29 16:48 2.0K trackDb.sql 2024-01-31 15:13 2.1K netHg38.sql 2020-08-17 13:28 2.1K netMm10.sql 2020-08-17 13:09 2.1K netMm39.sql 2020-09-08 13:46 2.1K all_est.sql 2020-08-18 11:45 2.1K all_mrna.sql 2020-08-18 06:08 2.1K xenoMrna.sql 2020-08-18 06:09 2.1K intronEst.sql 2020-08-18 11:45 2.1K refSeqAli.sql 2020-08-18 06:37 2.1K xenoRefSeqAli.sql 2020-08-18 06:37 2.1K tableList.txt.gz 2024-12-08 03:04 3.0K cytoBandIdeo.txt.gz 2020-07-17 20:10 4.7K chromInfo.txt.gz 2020-07-17 16:00 4.9K tableDescriptions.txt.gz 2024-12-07 02:04 5.5K ucscToINSDC.txt.gz 2020-07-29 14:00 6.7K chromAlias.txt.gz 2020-07-29 13:24 8.4K gap.txt.gz 2020-07-17 15:52 16K gold.txt.gz 2020-07-17 15:52 32K trackDb.txt.gz 2024-01-31 15:13 35K mrnaOrientInfo.txt.gz 2020-08-18 12:16 90K ensemblToGeneName.txt.gz 2021-05-25 14:22 94K ensemblSource.txt.gz 2021-05-25 14:23 135K refFlat.txt.gz 2020-08-18 06:37 168K refGene.txt.gz 2020-08-18 06:37 181K refSeqAli.txt.gz 2020-08-18 06:37 191K all_mrna.txt.gz 2020-08-18 06:08 232K ensGtp.txt.gz 2021-05-25 14:22 409K microsat.txt.gz 2020-07-28 07:50 594K cpgIslandExt.txt.gz 2020-07-28 09:15 1.0M cpgIslandExtUnmasked.txt.gz 2020-07-17 16:59 1.1M augustusGene.txt.gz 2020-07-29 16:48 2.3M ensGene.txt.gz 2021-05-25 14:22 2.9M genscan.txt.gz 2020-07-31 12:18 3.0M estOrientInfo.txt.gz 2020-08-18 11:45 4.1M intronEst.txt.gz 2020-08-18 11:45 8.8M xenoRefFlat.txt.gz 2020-08-18 06:37 10M xenoRefGene.txt.gz 2020-08-18 06:37 12M ensPep.txt.gz 2021-05-25 14:23 12M nestedRepeats.txt.gz 2020-07-18 06:33 14M all_est.txt.gz 2020-08-18 11:45 16M xenoRefSeqAli.txt.gz 2020-08-18 06:37 22M simpleRepeat.txt.gz 2020-07-17 17:05 22M chainMm39.txt.gz 2020-09-08 13:40 53M chainMm10.txt.gz 2020-08-17 13:03 55M netMm10.txt.gz 2020-08-17 13:09 59M netMm39.txt.gz 2020-09-08 13:46 59M netHg38.txt.gz 2020-08-17 13:28 64M rmsk.txt.gz 2020-07-18 06:31 122M windowmaskerSdust.txt.gz 2020-07-28 08:54 124M chainHg38.txt.gz 2020-08-17 13:19 204M xenoMrna.txt.gz 2020-08-18 06:09 221M chainMm39Link.txt.gz 2020-09-08 13:43 447M chainMm10Link.txt.gz 2020-08-17 13:06 457M chainHg38Link.txt.gz 2020-08-17 13:25 903M