This directory contains a dump of the UCSC genome annotation database for the Oct. 2013 (KORDI BalAcu1.0/balAcu1) assembly of the minke whale genome (balAcu1, KORDI BalAcu1.0 (GCA_000493695.1)) from the Genome Sequencing Consortium. 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/10769 http://www.ncbi.nlm.nih.gov/genome/assembly/78761 http://www.ncbi.nlm.nih.gov/bioproject/237330 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=balAcu1 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/balAcu1/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/balAcu1/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/balAcu1/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 balAcu1 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql balAcu1 --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 - xenoRefSeqAli.txt.gz 2020-08-18 08:08 41M xenoRefSeqAli.sql 2020-08-18 08:08 2.1K xenoRefGene.txt.gz 2020-08-18 08:08 40M xenoRefGene.sql 2020-08-18 08:08 2.0K xenoRefFlat.txt.gz 2020-08-18 08:08 36M xenoRefFlat.sql 2020-08-18 08:08 1.7K windowmaskerSdust.txt.gz 2014-04-11 15:18 123M windowmaskerSdust.sql 2014-04-11 15:18 1.5K ucscToRefSeq.txt.gz 2018-02-18 05:08 67K ucscToRefSeq.sql 2018-02-18 05:08 1.4K ucscToINSDC.txt.gz 2014-04-11 15:18 65K ucscToINSDC.sql 2014-04-11 15:18 1.4K trackDb.txt.gz 2024-01-31 15:13 33K trackDb.sql 2024-01-31 15:13 2.1K tableList.txt.gz 2024-09-01 03:31 2.2K tableList.sql 2024-09-01 03:31 1.6K tableDescriptions.txt.gz 2024-08-31 02:03 5.2K tableDescriptions.sql 2024-08-31 02:03 1.4K simpleRepeat.txt.gz 2014-04-11 15:18 16M simpleRepeat.sql 2014-04-11 15:18 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:26 645K seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K rmsk.txt.gz 2014-04-11 15:17 103M rmsk.sql 2014-04-11 15:17 1.9K nestedRepeats.txt.gz 2014-04-11 15:17 11M nestedRepeats.sql 2014-04-11 15:17 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.7M ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 7.2M ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75 ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.2M ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 619 ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:26 252K ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:26 2.7M ncbiRefSeq.sql 2020-05-10 03:26 1.9K microsat.txt.gz 2015-08-23 09:56 291K microsat.sql 2015-08-23 09:56 1.5K history.txt.gz 2014-04-11 15:17 404 history.sql 2014-04-11 15:17 1.6K hgFindSpec.txt.gz 2024-01-31 15:13 1.0K hgFindSpec.sql 2024-01-31 15:13 1.8K grp.txt.gz 2014-10-19 07:13 200 grp.sql 2014-10-19 07:13 1.3K gold.txt.gz 2014-04-11 15:18 3.0M gold.sql 2014-04-11 15:18 1.7K genscanSubopt.txt.gz 2014-04-11 15:18 5.9M genscanSubopt.sql 2014-04-11 15:18 1.6K genscan.txt.gz 2014-04-11 15:17 2.9M genscan.sql 2014-04-11 15:17 1.7K gc5BaseBw.txt.gz 2014-04-11 15:18 66 gc5BaseBw.sql 2014-04-11 15:18 1.3K gbLoaded.txt.gz 2020-08-18 08:08 11K gbLoaded.sql 2020-08-18 08:08 1.6K gap.txt.gz 2014-04-11 15:17 2.2M gap.sql 2014-04-11 15:17 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:26 91 extNcbiRefSeq.sql 2020-05-10 03:26 1.4K cytoBandIdeo.txt.gz 2014-04-11 15:17 41K cytoBandIdeo.sql 2014-04-11 15:17 1.5K cpgIslandExtUnmasked.txt.gz 2014-04-11 15:17 1.3M cpgIslandExtUnmasked.sql 2014-04-11 15:17 1.7K cpgIslandExt.txt.gz 2014-04-11 15:17 959K cpgIslandExt.sql 2014-04-11 15:17 1.7K chromInfo.txt.gz 2014-04-11 15:17 41K chromInfo.sql 2014-04-11 15:17 1.4K chromAlias.txt.gz 2018-02-18 05:08 104K chromAlias.sql 2018-02-18 05:08 1.4K bigFiles.txt.gz 2024-09-01 03:31 95 bigFiles.sql 2024-09-01 03:31 1.4K augustusGene.txt.gz 2015-07-26 10:13 2.2M augustusGene.sql 2015-07-26 10:13 1.9K