This directory contains a dump of the UCSC genome annotation database for the Oct. 2011 (Baylor Ttru_1.4/turTru2) assembly of the dolphin genome (turTru2, Baylor College of Medicine Ttru_1.4 (NCBI project 20365, GCA_000151865.2, WGS ABRN02)). 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/769 http://www.ncbi.nlm.nih.gov/genome/assembly/325108 http://www.ncbi.nlm.nih.gov/bioproject/20367 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=turTru2 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/turTru2/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/turTru2/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/turTru2/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 turTru2 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql turTru2 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' For conditions of use regarding the Dolphin genome sequence data, see http://www.hgsc.bcm.edu/content/conditions-use ----------------------------------------------------------------------------- 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 - augustusGene.sql 2019-01-03 13:30 1.9K augustusGene.txt.gz 2019-01-03 13:30 2.1M bigFiles.sql 2024-09-01 03:30 1.4K bigFiles.txt.gz 2024-09-01 03:30 68 chainBosTau7.sql 2019-01-03 13:30 1.7K chainBosTau7.txt.gz 2019-01-03 13:31 1.5G chainBosTau7Link.sql 2019-01-03 13:36 1.5K chainBosTau7Link.txt.gz 2019-01-03 13:42 4.4G chainMm10.sql 2019-01-03 13:59 1.7K chainMm10.txt.gz 2019-01-03 13:59 33M chainMm10Link.sql 2019-01-03 13:59 1.5K chainMm10Link.txt.gz 2019-01-03 13:59 326M chainMm39.sql 2020-11-24 20:19 1.7K chainMm39.txt.gz 2020-11-24 20:19 21M chainMm39Link.sql 2020-11-24 20:21 1.6K chainMm39Link.txt.gz 2020-11-24 20:21 291M chromInfo.sql 2019-01-03 14:01 1.4K chromInfo.txt.gz 2019-01-03 14:01 1.0M cpgIslandExt.sql 2019-01-03 14:01 1.7K cpgIslandExt.txt.gz 2019-01-03 14:01 966K cpgIslandExtUnmasked.sql 2019-01-03 14:01 1.7K cpgIslandExtUnmasked.txt.gz 2019-01-03 14:01 1.4M cytoBandIdeo.sql 2019-01-03 14:01 1.5K cytoBandIdeo.txt.gz 2019-01-03 14:01 1.0M gap.sql 2019-01-03 14:01 1.6K gap.txt.gz 2019-01-03 14:01 3.5M gbLoaded.sql 2020-08-20 17:43 1.6K gbLoaded.txt.gz 2020-08-20 17:43 14K gc5BaseBw.sql 2019-01-03 14:01 1.3K gc5BaseBw.txt.gz 2019-01-03 14:01 63 genscan.sql 2019-01-03 14:01 1.7K genscan.txt.gz 2019-01-03 14:01 2.9M gold.sql 2019-01-03 14:01 1.7K gold.txt.gz 2019-01-03 14:01 6.6M grp.sql 2019-01-03 14:01 1.3K grp.txt.gz 2019-01-03 14:01 208 hgFindSpec.sql 2023-03-28 13:54 1.8K hgFindSpec.txt.gz 2023-03-28 13:54 581 history.sql 2019-01-03 14:01 1.6K history.txt.gz 2019-01-03 14:01 561 microsat.sql 2019-01-03 14:01 1.5K microsat.txt.gz 2019-01-03 14:01 458K nestedRepeats.sql 2019-01-03 14:01 1.9K nestedRepeats.txt.gz 2019-01-03 14:01 11M netBosTau7.sql 2019-01-03 14:01 2.1K netBosTau7.txt.gz 2019-01-03 14:01 61M netMm10.sql 2019-01-03 14:01 2.1K netMm10.txt.gz 2019-01-03 14:01 61M netMm39.sql 2020-11-24 20:24 2.1K netMm39.txt.gz 2020-11-24 20:24 61M rmsk.sql 2019-01-03 14:01 1.9K rmsk.txt.gz 2019-01-03 14:01 106M simpleRepeat.sql 2019-01-03 14:02 1.9K simpleRepeat.txt.gz 2019-01-03 14:02 16M tableDescriptions.sql 2024-08-31 02:04 1.4K tableDescriptions.txt.gz 2024-08-31 02:04 4.8K tableList.sql 2024-09-01 03:30 1.6K tableList.txt.gz 2024-09-01 03:30 2.1K trackDb.sql 2023-03-28 13:54 2.1K trackDb.txt.gz 2023-03-28 13:54 35K ucscToINSDC.sql 2019-01-03 14:02 1.4K ucscToINSDC.txt.gz 2019-01-03 14:02 1.6M windowmaskerSdust.sql 2019-01-03 14:02 1.5K windowmaskerSdust.txt.gz 2019-01-03 14:02 121M xenoRefFlat.sql 2020-08-20 17:29 1.7K xenoRefFlat.txt.gz 2020-08-20 17:29 34M xenoRefGene.sql 2020-08-20 17:29 2.0K xenoRefGene.txt.gz 2020-08-20 17:29 38M xenoRefSeqAli.sql 2020-08-20 17:29 2.1K xenoRefSeqAli.txt.gz 2020-08-20 17:29 42M