This directory contains a dump of the UCSC genome annotation database for the Dec. 2013 (GRCh38/hg38) assembly of the human genome (hg38, GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) . 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/51 http://www.ncbi.nlm.nih.gov/genome/assembly/883148 http://www.ncbi.nlm.nih.gov/bioproject/31257 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=hg38 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/hg38/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/hg38/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/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 hg38 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql hg38 --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 - affyGnf1h.sql 2015-05-11 01:50 2.1K affyGnf1h.txt.gz 2015-05-11 01:50 596K affyU95.sql 2015-05-11 01:50 2.1K affyU95.txt.gz 2015-05-11 01:50 2.1M affyU133.sql 2015-05-11 01:50 2.1K affyU133.txt.gz 2015-05-11 01:50 4.0M all_est.sql 2019-10-20 09:33 2.1K all_est.txt.gz 2019-10-20 09:33 432M all_mrna.sql 2020-08-17 18:38 2.1K all_mrna.txt.gz 2020-08-17 18:38 167M all_sts_primer.sql 2015-09-07 06:44 2.1K all_sts_primer.txt.gz 2015-09-07 06:44 9.6M all_sts_seq.sql 2015-09-07 06:44 2.1K all_sts_seq.txt.gz 2015-09-07 06:44 4.0M altLocations.sql 2022-11-03 14:54 1.5K altLocations.txt.gz 2022-11-03 14:54 11K altSeqLiftOverPsl.sql 2022-11-03 16:16 2.2K altSeqLiftOverPsl.txt.gz 2022-11-03 16:16 570K altSeqLiftOverPslP3.sql 2015-06-01 02:23 2.1K altSeqLiftOverPslP3.txt.gz 2015-06-01 02:23 18K altSeqLiftOverPslP6.sql 2016-03-13 03:31 2.1K altSeqLiftOverPslP6.txt.gz 2016-03-13 03:31 26K augustusGene.sql 2022-10-18 23:39 2.0K augustusGene.txt.gz 2022-10-18 23:39 2.6M bigFiles.sql 2024-10-06 03:39 1.4K bigFiles.txt.gz 2024-10-06 03:39 2.2K bioCycMapDesc.sql 2024-04-02 12:42 1.4K bioCycMapDesc.txt.gz 2024-04-02 12:42 5.5K bioCycPathway.sql 2024-04-02 12:42 1.5K bioCycPathway.txt.gz 2024-04-02 12:42 22K ccdsGene.sql 2019-10-20 09:43 1.9K ccdsGene.txt.gz 2019-10-20 09:43 2.1M ccdsInfo.sql 2019-10-20 09:35 1.4K ccdsInfo.txt.gz 2019-10-20 09:35 1.3M ccdsKgMap.sql 2021-01-26 13:10 1.5K ccdsKgMap.txt.gz 2021-01-26 13:10 819K ccdsNotes.sql 2019-10-20 09:35 1.4K ccdsNotes.txt.gz 2019-10-20 09:35 20K ceBlastTab.sql 2024-04-02 12:42 1.7K ceBlastTab.txt.gz 2024-04-02 12:42 118K centromeres.sql 2014-08-17 12:08 1.5K centromeres.txt.gz 2014-08-17 12:08 1.5K cgapAlias.sql 2021-01-26 16:50 1.4K cgapAlias.txt.gz 2021-01-26 16:50 1.3M cgapBiocDesc.sql 2021-01-26 16:50 1.4K cgapBiocDesc.txt.gz 2021-01-26 16:50 6.8K cgapBiocPathway.sql 2021-01-26 16:50 1.4K cgapBiocPathway.txt.gz 2021-01-26 16:50 25K chainAquChr2.sql 2019-02-17 03:24 1.7K chainAquChr2.txt.gz 2019-02-17 03:24 17M chainAquChr2Link.sql 2019-02-17 03:23 1.5K chainAquChr2Link.txt.gz 2019-02-17 03:23 144M chainBosTau9.sql 2019-06-09 03:29 1.7K chainBosTau9.txt.gz 2019-06-09 03:29 158M chainBosTau9Link.sql 2019-06-09 03:30 1.5K chainBosTau9Link.txt.gz 2019-06-09 03:31 810M chainCalJac4.sql 2020-09-03 23:43 1.7K chainCalJac4.txt.gz 2020-09-03 23:43 545M chainCalJac4Link.sql 2020-09-03 23:58 1.6K chainCalJac4Link.txt.gz 2020-09-03 23:58 1.6G chainCanFam4.sql 2020-04-03 00:54 1.7K chainCanFam4.txt.gz 2020-04-03 00:54 402M chainCanFam4Link.sql 2020-04-03 01:06 1.6K chainCanFam4Link.txt.gz 2020-04-03 01:06 1.2G chainCanFam6.sql 2021-05-17 21:54 1.7K chainCanFam6.txt.gz 2021-05-17 21:54 217M chainCanFam6Link.sql 2021-05-17 22:02 1.6K chainCanFam6Link.txt.gz 2021-05-17 22:02 939M chainChlSab2.sql 2016-10-30 08:17 1.7K chainChlSab2.txt.gz 2016-10-30 08:17 18M chainChlSab2Link.sql 2016-10-30 08:17 1.5K chainChlSab2Link.txt.gz 2016-10-30 08:17 191M chainCriGriChoV2.sql 2019-06-09 03:34 1.7K 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1.3M chainHprcGCA_018466835v1.sql 2023-10-14 13:54 1.8K chainHprcGCA_018466835v1.txt.gz 2023-10-14 13:54 11K chainHprcGCA_018466835v1Link.sql 2023-10-14 13:54 1.6K chainHprcGCA_018466835v1Link.txt.gz 2023-10-14 13:54 9.5M chainHprcGCA_018466845v1.sql 2023-10-14 13:54 1.8K chainHprcGCA_018466845v1.txt.gz 2023-10-14 13:54 11K chainHprcGCA_018466845v1Link.sql 2023-10-14 13:54 1.6K chainHprcGCA_018466845v1Link.txt.gz 2023-10-14 13:54 9.3M chainHprcGCA_018466855v1.sql 2023-10-14 13:54 1.8K chainHprcGCA_018466855v1.txt.gz 2023-10-14 13:54 14K chainHprcGCA_018466855v1Link.sql 2023-10-14 13:54 1.6K chainHprcGCA_018466855v1Link.txt.gz 2023-10-14 13:54 9.5M chainHprcGCA_018466985v1.sql 2023-10-14 13:54 1.8K chainHprcGCA_018466985v1.txt.gz 2023-10-14 13:54 16K chainHprcGCA_018466985v1Link.sql 2023-10-14 13:55 1.6K chainHprcGCA_018466985v1Link.txt.gz 2023-10-14 13:55 9.5M chainHprcGCA_018467005v1.sql 2023-10-14 13:55 1.8K chainHprcGCA_018467005v1.txt.gz 2023-10-14 13:55 11K 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