This directory contains a dump of the UCSC genome annotation database for the Apr. 2018 (ARS-UCD1.2/bosTau9) assembly of the cow genome (bosTau9, USDA ARS) . 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/82 https://www.ncbi.nlm.nih.gov/genome/assembly/1677391 https://www.ncbi.nlm.nih.gov/bioproject/391427 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=bosTau9 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/bosTau9/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/bosTau9/database/ . For a single file, e.g. gc5Base.txt.gz rsync -avzP rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/gc5Base.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/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 bosTau9 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql bosTau9 --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 - gap.txt.gz 2019-06-07 10:46 28 gc5BaseBw.txt.gz 2019-06-07 10:46 66 crisprAllTargets.txt.gz 2022-03-20 13:48 69 ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 extNcbiRefSeq.txt.gz 2020-05-10 03:26 89 bigFiles.txt.gz 2024-09-01 03:06 119 grp.txt.gz 2019-06-07 10:46 213 history.txt.gz 2019-06-07 10:47 912 hgFindSpec.txt.gz 2024-01-31 15:13 1.3K gc5BaseBw.sql 2019-06-07 10:46 1.3K ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K crisprAllTargets.sql 2022-03-20 13:48 1.3K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ensPep.sql 2021-05-25 14:22 1.3K grp.sql 2019-06-07 10:46 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ensemblSource.sql 2021-05-25 14:22 1.4K chromInfo.sql 2019-06-07 10:46 1.4K bigFiles.sql 2024-09-01 03:06 1.4K ensemblToGeneName.sql 2021-05-25 14:20 1.4K chromAlias.sql 2020-04-12 03:25 1.4K ucscToINSDC.sql 2019-06-07 10:47 1.4K ucscToRefSeq.sql 2019-06-07 10:47 1.4K extNcbiRefSeq.sql 2020-05-10 03:26 1.4K ensGtp.sql 2021-05-25 14:20 1.4K tableDescriptions.sql 2024-08-31 02:04 1.5K microsat.sql 2019-06-07 10:47 1.5K windowmaskerSdust.sql 2019-06-07 10:47 1.5K cytoBandIdeo.sql 2019-06-07 10:46 1.5K chainHg38Link.sql 2019-06-07 10:39 1.5K chainMm10Link.sql 2019-06-07 10:43 1.5K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K chainMm39Link.sql 2020-11-23 19:23 1.6K history.sql 2019-06-07 10:47 1.6K gbLoaded.sql 2019-06-16 03:21 1.6K tableList.sql 2024-09-01 03:06 1.6K gap.sql 2019-06-07 10:46 1.6K gold.sql 2019-06-07 10:47 1.7K genscan.sql 2019-06-07 10:47 1.7K cpgIslandExt.sql 2019-06-07 10:46 1.7K chainHg38.sql 2019-06-07 10:38 1.7K chainMm10.sql 2019-06-07 10:43 1.7K refFlat.sql 2019-06-07 10:46 1.7K cpgIslandExtUnmasked.sql 2019-06-07 10:46 1.7K xenoRefFlat.sql 2019-06-07 10:47 1.7K chainMm39.sql 2020-11-23 19:20 1.7K hgFindSpec.sql 2024-01-31 15:13 1.8K estOrientInfo.sql 2019-06-16 03:21 1.8K mrnaOrientInfo.sql 2019-06-07 10:37 1.8K rmsk.sql 2019-06-07 10:46 1.9K refGene.sql 2019-06-07 10:46 1.9K simpleRepeat.sql 2019-06-07 10:47 1.9K ncbiRefSeq.sql 2020-05-10 03:26 1.9K nestedRepeats.sql 2019-06-07 10:37 1.9K xenoRefGene.sql 2019-06-07 10:47 1.9K augustusGene.sql 2019-06-07 10:37 1.9K ensGene.sql 2021-05-25 14:20 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K trackDb.sql 2024-01-31 15:13 2.1K netHg38.sql 2019-06-07 10:37 2.1K netMm10.sql 2019-06-07 10:43 2.1K all_est.sql 2019-06-16 03:21 2.1K intronEst.sql 2019-06-16 03:21 2.1K all_mrna.sql 2019-06-07 10:37 2.1K refSeqAli.sql 2019-06-07 10:46 2.1K netMm39.sql 2020-11-23 19:26 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K xenoRefSeqAli.sql 2019-06-07 10:47 2.1K tableList.txt.gz 2024-09-01 03:06 3.5K gbLoaded.txt.gz 2019-06-16 03:21 4.2K tableDescriptions.txt.gz 2024-08-31 02:04 6.3K cytoBandIdeo.txt.gz 2019-06-07 10:46 13K chromInfo.txt.gz 2019-06-07 10:46 14K ucscToRefSeq.txt.gz 2019-06-07 10:47 19K ucscToINSDC.txt.gz 2019-06-07 10:47 20K chromAlias.txt.gz 2020-04-12 03:25 21K gold.txt.gz 2019-06-07 10:47 27K trackDb.txt.gz 2024-01-31 15:13 60K ensemblSource.txt.gz 2021-05-25 14:22 134K ensemblToGeneName.txt.gz 2021-05-25 14:20 245K microsat.txt.gz 2019-06-07 10:47 278K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 441K ensGtp.txt.gz 2021-05-25 14:20 507K mrnaOrientInfo.txt.gz 2019-06-07 10:37 569K cpgIslandExt.txt.gz 2019-06-07 10:46 815K cpgIslandExtUnmasked.txt.gz 2019-06-07 10:46 936K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 1.1M refFlat.txt.gz 2019-06-07 10:46 1.3M ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 1.4M refSeqAli.txt.gz 2019-06-07 10:46 1.4M refGene.txt.gz 2019-06-07 10:46 1.4M all_mrna.txt.gz 2019-06-07 10:37 1.5M augustusGene.txt.gz 2019-06-07 10:37 2.3M ncbiRefSeqLink.txt.gz 2020-05-10 03:26 2.3M ensGene.txt.gz 2021-05-25 14:20 2.9M genscan.txt.gz 2019-06-07 10:47 3.0M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.1M ncbiRefSeq.txt.gz 2020-05-10 03:26 3.8M ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 5.5M ensPep.txt.gz 2021-05-25 14:22 13M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 13M simpleRepeat.txt.gz 2019-06-07 10:47 15M nestedRepeats.txt.gz 2019-06-07 10:37 16M estOrientInfo.txt.gz 2019-06-16 03:21 18M xenoRefFlat.txt.gz 2019-06-07 10:47 20M xenoRefSeqAli.txt.gz 2019-06-07 10:47 21M xenoRefGene.txt.gz 2019-06-07 10:47 21M intronEst.txt.gz 2019-06-16 03:21 37M netMm10.txt.gz 2019-06-07 10:43 55M netMm39.txt.gz 2020-11-23 19:26 55M all_est.txt.gz 2019-06-16 03:21 58M chainMm10.txt.gz 2019-06-07 10:43 64M netHg38.txt.gz 2019-06-07 10:38 65M chainMm39.txt.gz 2020-11-23 19:20 68M windowmaskerSdust.txt.gz 2019-06-07 10:47 119M rmsk.txt.gz 2019-06-07 10:46 142M chainHg38.txt.gz 2019-06-07 10:38 156M chainMm10Link.txt.gz 2019-06-07 10:44 495M chainMm39Link.txt.gz 2020-11-23 19:23 502M chainHg38Link.txt.gz 2019-06-07 10:40 796M