This directory contains a dump of the UCSC genome annotation database for the May. 2010 (Genofisk GadMor_May2010/gadMor1) assembly of the atlantic cod genome (gadMor1, Genofisk GadMor_May2010 (GCA_000231765.1)). 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/2661 http://www.ncbi.nlm.nih.gov/genome/assembly/311358 http://www.ncbi.nlm.nih.gov/bioproject/41391 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=gadMor1 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/gadMor1/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/gadMor1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/gadMor1/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 gadMor1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql gadMor1 --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 - all_est.sql 2016-05-15 08:41 2.1K all_est.txt.gz 2016-05-15 08:41 14M all_mrna.sql 2020-08-19 10:05 2.1K all_mrna.txt.gz 2020-08-19 10:05 3.1M augustusGene.sql 2015-07-26 13:39 1.9K augustusGene.txt.gz 2015-07-26 13:39 3.0M bigFiles.sql 2024-10-27 03:41 1.4K bigFiles.txt.gz 2024-10-27 03:41 68 chainFr3.sql 2012-11-06 14:09 1.7K chainFr3.txt.gz 2012-11-06 14:09 20M chainFr3Link.sql 2012-11-06 14:10 1.5K chainFr3Link.txt.gz 2012-11-06 14:10 93M chainMm10.sql 2012-11-06 14:12 1.7K chainMm10.txt.gz 2012-11-06 14:12 7.1M chainMm10Link.sql 2012-11-06 14:11 1.5K chainMm10Link.txt.gz 2012-11-06 14:11 35M chromAlias.sql 2018-08-05 06:36 1.4K chromAlias.txt.gz 2018-08-05 06:36 2.1M chromInfo.sql 2012-11-06 14:10 1.4K chromInfo.txt.gz 2012-11-06 14:10 1.8M cpgIslandExt.sql 2012-11-06 14:10 1.7K cpgIslandExt.txt.gz 2012-11-06 14:10 1.0M cpgIslandExtUnmasked.sql 2014-06-01 13:15 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:15 1.8M cytoBandIdeo.sql 2013-04-28 15:14 1.5K cytoBandIdeo.txt.gz 2013-04-28 15:14 1.9M ensGene.sql 2019-02-10 03:41 1.9K ensGene.txt.gz 2019-02-10 03:41 2.9M ensGtp.sql 2019-02-10 03:41 1.4K ensGtp.txt.gz 2019-02-10 03:41 230K ensPep.sql 2019-02-10 03:41 1.3K ensPep.txt.gz 2019-02-10 03:41 5.5M ensemblGeneScaffold.sql 2019-02-10 03:41 1.7K ensemblGeneScaffold.txt.gz 2019-02-10 03:41 2.6M ensemblSource.sql 2019-02-10 03:41 1.4K ensemblSource.txt.gz 2019-02-10 03:41 61K ensemblToGeneName.sql 2019-02-10 03:41 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:41 121K estOrientInfo.sql 2016-05-15 08:41 1.8K estOrientInfo.txt.gz 2016-05-15 08:41 3.7M gap.sql 2012-11-06 14:11 1.6K gap.txt.gz 2012-11-06 14:11 1.7M gbLoaded.sql 2020-08-19 10:11 1.6K gbLoaded.txt.gz 2020-08-19 10:11 44K gc5BaseBw.sql 2012-11-06 14:11 1.3K gc5BaseBw.txt.gz 2012-11-06 14:11 63 genscan.sql 2012-11-06 14:10 1.7K genscan.txt.gz 2012-11-06 14:10 1.9M gold.sql 2012-11-06 14:10 1.7K gold.txt.gz 2012-11-06 14:10 6.1M grp.sql 2014-03-02 03:41 1.3K grp.txt.gz 2014-03-02 03:41 208 hgFindSpec.sql 2023-03-28 13:49 1.8K hgFindSpec.txt.gz 2023-03-28 13:49 837 history.sql 2012-11-06 14:10 1.6K history.txt.gz 2012-11-06 14:10 551 intronEst.sql 2016-05-15 08:41 2.1K intronEst.txt.gz 2016-05-15 08:41 4.7M microsat.sql 2015-08-23 16:40 1.5K microsat.txt.gz 2015-08-23 16:40 1.4M mrnaOrientInfo.sql 2020-08-19 10:05 1.8K mrnaOrientInfo.txt.gz 2020-08-19 10:05 841K nestedRepeats.sql 2012-11-06 14:10 1.9K nestedRepeats.txt.gz 2012-11-06 14:10 304K netFr3.sql 2012-11-06 14:10 2.1K netFr3.txt.gz 2012-11-06 14:10 14M netMm10.sql 2012-11-06 14:10 2.1K netMm10.txt.gz 2012-11-06 14:10 5.5M rmsk.sql 2012-11-06 14:11 1.9K rmsk.txt.gz 2012-11-06 14:11 15M simpleRepeat.sql 2012-11-06 14:10 1.9K simpleRepeat.txt.gz 2012-11-06 14:10 21M tableDescriptions.sql 2024-10-26 02:03 1.4K tableDescriptions.txt.gz 2024-10-26 02:03 5.5K tableList.sql 2024-10-27 03:41 1.6K tableList.txt.gz 2024-10-27 03:41 2.5K trackDb.sql 2023-03-28 13:49 2.1K trackDb.txt.gz 2023-03-28 13:49 38K ucscToEnsembl.sql 2013-08-11 03:46 1.4K ucscToEnsembl.txt.gz 2013-08-11 03:46 2.0M ucscToINSDC.sql 2013-09-15 13:09 1.4K ucscToINSDC.txt.gz 2013-09-15 13:09 3.0M windowmaskerSdust.sql 2012-11-06 14:10 1.5K windowmaskerSdust.txt.gz 2012-11-06 14:10 30M xenoRefFlat.sql 2020-08-19 10:11 1.7K xenoRefFlat.txt.gz 2020-08-19 10:11 27M xenoRefGene.sql 2020-08-19 10:11 2.0K xenoRefGene.txt.gz 2020-08-19 10:11 31M xenoRefSeqAli.sql 2020-08-19 10:11 2.1K xenoRefSeqAli.txt.gz 2020-08-19 10:11 29M