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 - bigFiles.txt.gz 2024-12-08 03:36 2.2K bigFiles.sql 2024-12-08 03:36 1.4K tableList.txt.gz 2024-12-08 03:36 101K tableList.sql 2024-12-08 03:36 1.6K tableDescriptions.txt.gz 2024-12-07 02:03 55K tableDescriptions.sql 2024-12-07 02:03 1.5K ncbiRefSeqHgmd.txt.gz 2024-12-05 03:05 1.8M ncbiRefSeqHgmd.sql 2024-12-05 03:05 2.0K gwasCatalog.txt.gz 2024-12-04 04:48 49M gwasCatalog.sql 2024-12-04 04:48 2.1K geneReviewsDetail.txt.gz 2024-12-03 08:03 31K geneReviewsDetail.sql 2024-12-03 08:03 1.5K geneReviews.txt.gz 2024-12-03 08:01 30K geneReviews.sql 2024-12-03 08:01 1.5K relatedTrack.txt.gz 2024-11-08 15:28 914 relatedTrack.sql 2024-11-08 15:28 1.5K hgFindSpec.txt.gz 2024-11-08 15:27 12K hgFindSpec.sql 2024-11-08 15:27 1.8K trackDb.txt.gz 2024-11-08 15:27 1.2M trackDb.sql 2024-11-08 15:27 2.1K wgEncodeGencodeTranscriptionSupportLevelV47.txt.gz 2024-10-17 22:58 1.2M wgEncodeGencodeTranscriptionSupportLevelV47.sql 2024-10-17 22:58 1.5K wgEncodeGencodeExonSupportV47.txt.gz 2024-10-17 22:44 61M wgEncodeGencodeExonSupportV47.sql 2024-10-17 22:44 1.6K wgEncodeGencodeTagV47.txt.gz 2024-10-17 22:42 3.1M wgEncodeGencodeTagV47.sql 2024-10-17 22:42 1.4K wgEncodeGencodeAttrsV47.txt.gz 2024-10-17 22:41 9.2M wgEncodeGencodeAttrsV47.sql 2024-10-17 22:41 2.1K wgEncodeGencodeCompV47.txt.gz 2024-10-17 22:41 14M wgEncodeGencodeCompV47.sql 2024-10-17 22:41 2.0K wgEncodeGencodeBasicV47.txt.gz 2024-10-17 22:41 7.3M wgEncodeGencodeBasicV47.sql 2024-10-17 22:41 2.0K wgEncodeGencodePseudoGeneV47.txt.gz 2024-10-17 22:41 640K wgEncodeGencodePseudoGeneV47.sql 2024-10-17 22:41 2.0K wgEncodeGencodeEntrezGeneV47.txt.gz 2024-10-17 22:41 1.4M wgEncodeGencodeEntrezGeneV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodePubMedV47.txt.gz 2024-10-17 22:41 1.6M wgEncodeGencodePubMedV47.sql 2024-10-17 22:41 1.4K wgEncodeGencodeTranscriptSourceV47.txt.gz 2024-10-17 22:41 1.8M wgEncodeGencodeTranscriptSourceV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodeAnnotationRemarkV47.txt.gz 2024-10-17 22:41 1.4M wgEncodeGencodeAnnotationRemarkV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodeRefSeqV47.txt.gz 2024-10-17 22:41 938K wgEncodeGencodeRefSeqV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodeUniProtV47.txt.gz 2024-10-17 22:41 1.2M wgEncodeGencodeUniProtV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodeGeneSymbolV47.txt.gz 2024-10-17 22:41 1.8M wgEncodeGencodeGeneSymbolV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodePdbV47.txt.gz 2024-10-17 22:41 1.1M wgEncodeGencodePdbV47.sql 2024-10-17 22:41 1.4K wgEncodeGencodeTranscriptSupportV47.txt.gz 2024-10-17 22:41 116K wgEncodeGencodeTranscriptSupportV47.sql 2024-10-17 22:41 1.5K wgEncodeGencodeGeneSourceV47.txt.gz 2024-10-17 22:41 408K wgEncodeGencodeGeneSourceV47.sql 2024-10-17 22:41 1.4K wgEncodeGencodePolyaV47.txt.gz 2024-10-17 22:38 1.7M wgEncodeGencodePolyaV47.sql 2024-10-17 22:38 2.0K ncbiRefSeqPepTable.txt.gz 2024-09-11 10:20 24M ncbiRefSeqPepTable.sql 2024-09-11 10:20 1.4K seqNcbiRefSeq.txt.gz 2024-09-11 09:49 2.8M seqNcbiRefSeq.sql 2024-09-11 09:49 1.6K ncbiRefSeqOther.txt.gz 2024-09-11 09:49 72 ncbiRefSeqOther.sql 2024-09-11 09:49 1.3K ncbiRefSeqCds.txt.gz 2024-09-11 09:49 945K ncbiRefSeqCds.sql 2024-09-11 09:49 1.4K extNcbiRefSeq.txt.gz 2024-09-11 09:48 88 extNcbiRefSeq.sql 2024-09-11 09:48 1.5K ncbiRefSeqPsl.txt.gz 2024-09-11 08:33 11M ncbiRefSeqPsl.sql 2024-09-11 08:33 2.2K ncbiRefSeqLink.txt.gz 2024-09-11 08:32 12M ncbiRefSeqLink.sql 2024-09-11 08:32 2.1K ncbiRefSeqPredicted.txt.gz 2024-09-11 08:32 3.7M ncbiRefSeqPredicted.sql 2024-09-11 08:32 2.0K ncbiRefSeqSelect.txt.gz 2024-09-11 08:32 2.4M ncbiRefSeqSelect.sql 2024-09-11 08:32 2.0K ncbiRefSeqCurated.txt.gz 2024-09-11 08:32 4.5M ncbiRefSeqCurated.sql 2024-09-11 08:32 2.0K ncbiRefSeq.txt.gz 2024-09-11 08:32 7.0M ncbiRefSeq.sql 2024-09-11 08:32 2.0K knownToMyGene2.txt.gz 2024-08-20 08:46 205K knownToMyGene2.sql 2024-08-20 08:46 1.4K ucscScop.txt.gz 2024-08-19 16:06 2.4M ucscScop.sql 2024-08-19 16:06 1.5K ucscGenePfam.txt.gz 2024-08-19 16:06 1.6M ucscGenePfam.sql 2024-08-19 16:06 1.8K spMrna.txt.gz 2024-08-19 16:06 850K spMrna.sql 2024-08-19 16:06 1.4K scopDesc.txt.gz 2024-08-19 16:06 32K scopDesc.sql 2024-08-19 16:06 1.4K scBlastTab.txt.gz 2024-08-19 16:06 62K scBlastTab.sql 2024-08-19 16:06 1.7K rnBlastTab.txt.gz 2024-08-19 16:06 1.9M rnBlastTab.sql 2024-08-19 16:06 1.7K pfamDesc.txt.gz 2024-08-19 16:06 308K pfamDesc.sql 2024-08-19 16:06 1.5K mmBlastTab.txt.gz 2024-08-19 16:06 2.0M mmBlastTab.sql 2024-08-19 16:06 1.7K knownToWikipedia.txt.gz 2024-08-19 16:06 935K knownToWikipedia.sql 2024-08-19 16:06 1.4K knownToVisiGene.txt.gz 2024-08-19 16:06 39K knownToVisiGene.sql 2024-08-19 16:06 1.5K knownToU95.txt.gz 2024-08-19 16:06 522K knownToU95.sql 2024-08-19 16:06 1.4K knownToU133.txt.gz 2024-08-19 16:06 1.0M knownToU133.sql 2024-08-19 16:06 1.4K knownToTag.txt.gz 2024-08-19 16:06 3.1M knownToTag.sql 2024-08-19 16:06 1.4K knownToSuper.txt.gz 2024-08-19 16:06 3.0M knownToSuper.sql 2024-08-19 16:06 1.5K knownToRefSeq.txt.gz 2024-08-19 16:06 1.9M knownToRefSeq.sql 2024-08-19 16:06 1.4K knownToPfam.txt.gz 2024-08-19 16:06 832K knownToPfam.sql 2024-08-19 16:06 1.4K knownToNextProt.txt.gz 2024-08-19 16:06 310K knownToNextProt.sql 2024-08-19 16:06 1.4K knownToMupit.txt.gz 2024-08-19 16:06 267K knownToMupit.sql 2024-08-19 16:06 1.4K knownToMrnaSingle.txt.gz 2024-08-19 16:06 1.7M knownToMrnaSingle.sql 2024-08-19 16:06 1.4K knownToMrna.txt.gz 2024-08-19 16:06 26M knownToMrna.sql 2024-08-19 16:06 1.4K knownToMalacards.txt.gz 2024-08-19 16:04 1.5M knownToMalacards.sql 2024-08-19 16:04 1.4K knownToLocusLink.txt.gz 2024-08-19 16:04 1.6M knownToLocusLink.sql 2024-08-19 16:04 1.4K knownToHprd.txt.gz 2024-08-19 16:04 233K knownToHprd.sql 2024-08-19 16:04 1.4K knownToGtex.txt.gz 2024-08-19 16:04 1.8M knownToGtex.sql 2024-08-19 16:04 1.4K knownToGnfAtlas2.txt.gz 2024-08-19 16:04 858K knownToGnfAtlas2.sql 2024-08-19 16:04 1.4K knownToGencodeV47.txt.gz 2024-08-19 16:04 2.0M knownToGencodeV47.sql 2024-08-19 16:04 1.4K knownToEnsembl.txt.gz 2024-08-19 16:04 2.0M knownToEnsembl.sql 2024-08-19 16:04 1.4K knownIsoforms.txt.gz 2024-08-19 16:04 1.8M knownIsoforms.sql 2024-08-19 16:04 1.4K knownCds.txt.gz 2024-08-19 16:03 2.0M knownCds.sql 2024-08-19 16:03 1.5K knownCanonical.txt.gz 2024-08-19 16:03 1.7M knownCanonical.sql 2024-08-19 16:03 1.6K knownBlastTab.txt.gz 2024-08-19 16:03 194M knownBlastTab.sql 2024-08-19 16:03 1.7K knownAttrs.txt.gz 2024-08-19 16:00 6.7M knownAttrs.sql 2024-08-19 16:00 1.8K knownAlt.txt.gz 2024-08-19 16:00 3.5M knownAlt.sql 2024-08-19 16:00 1.6K kgV46ToKgV47.txt.gz 2024-08-19 16:00 4.1M kgV46ToKgV47.sql 2024-08-19 16:00 1.6K kgTargetAli.txt.gz 2024-08-19 16:00 21M kgTargetAli.sql 2024-08-19 16:00 2.2K kgSpAlias.txt.gz 2024-08-19 16:00 15M kgSpAlias.sql 2024-08-19 16:00 1.5K kgProtAlias.txt.gz 2024-08-19 15:59 4.4M kgProtAlias.sql 2024-08-19 15:59 1.5K kgColor.txt.gz 2024-08-19 15:59 1.2M kgColor.sql 2024-08-19 15:59 1.4K kgAlias.txt.gz 2024-08-19 15:59 14M kgAlias.sql 2024-08-19 15:59 1.4K humanWankerP2P.txt.gz 2024-08-19 15:59 2.6M humanWankerP2P.sql 2024-08-19 15:59 1.4K humanVidalP2P.txt.gz 2024-08-19 15:59 6.0M humanVidalP2P.sql 2024-08-19 15:59 1.4K humanHprdP2P.txt.gz 2024-08-19 15:59 44M humanHprdP2P.sql 2024-08-19 15:59 1.4K gnfU95Distance.txt.gz 2024-08-19 15:57 496M gnfU95Distance.sql 2024-08-19 15:57 1.4K gnfAtlas2Distance.txt.gz 2024-08-19 15:42 822M gnfAtlas2Distance.sql 2024-08-19 15:42 1.4K foldUtr5.txt.gz 2024-08-19 15:16 12M foldUtr5.sql 2024-08-19 15:16 1.4K foldUtr3.txt.gz 2024-08-19 15:16 54M foldUtr3.sql 2024-08-19 15:16 1.4K drBlastTab.txt.gz 2024-08-19 15:16 357K drBlastTab.sql 2024-08-19 15:16 1.7K dmBlastTab.txt.gz 2024-08-19 15:16 155K dmBlastTab.sql 2024-08-19 15:16 1.7K ceBlastTab.txt.gz 2024-08-19 15:16 118K ceBlastTab.sql 2024-08-19 15:16 1.7K bioCycPathway.txt.gz 2024-08-19 15:16 22K bioCycPathway.sql 2024-08-19 15:16 1.5K bioCycMapDesc.txt.gz 2024-08-19 15:16 5.5K bioCycMapDesc.sql 2024-08-19 15:16 1.4K knownGenePep.txt.gz 2024-08-19 15:16 9.6M knownGenePep.sql 2024-08-19 15:16 1.4K knownGeneMrna.txt.gz 2024-08-19 15:16 71M knownGeneMrna.sql 2024-08-19 15:16 1.4K knownGeneExt.txt.gz 2024-08-19 15:16 15M knownGeneExt.sql 2024-08-19 15:16 2.0K knownGene.txt.gz 2024-08-19 15:16 15M knownGene.sql 2024-08-19 15:16 2.0K kgXref.txt.gz 2024-08-19 15:16 11M kgXref.sql 2024-08-19 15:16 1.9K grp.txt.gz 2024-07-23 17:40 303 grp.sql 2024-07-23 17:40 1.5K wgEncodeGencodeTranscriptionSupportLevelV46.txt.gz 2024-05-13 11:58 892K wgEncodeGencodeTranscriptionSupportLevelV46.sql 2024-05-13 11:58 1.5K wgEncodeGencodeExonSupportV46.txt.gz 2024-05-13 11:42 60M wgEncodeGencodeExonSupportV46.sql 2024-05-13 11:42 1.6K wgEncodeGencodeTagV46.txt.gz 2024-05-13 11:40 2.3M wgEncodeGencodeTagV46.sql 2024-05-13 11:40 1.4K wgEncodeGencodeAttrsV46.txt.gz 2024-05-13 11:40 7.8M wgEncodeGencodeAttrsV46.sql 2024-05-13 11:40 2.1K wgEncodeGencodeCompV46.txt.gz 2024-05-13 11:40 10M wgEncodeGencodeCompV46.sql 2024-05-13 11:40 2.0K wgEncodeGencodePseudoGeneV46.txt.gz 2024-05-13 11:40 640K wgEncodeGencodePseudoGeneV46.sql 2024-05-13 11:40 2.0K wgEncodeGencodeBasicV46.txt.gz 2024-05-13 11:40 5.7M wgEncodeGencodeBasicV46.sql 2024-05-13 11:40 2.0K wgEncodeGencodeEntrezGeneV46.txt.gz 2024-05-13 11:39 1.2M wgEncodeGencodeEntrezGeneV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodeTranscriptSupportV46.txt.gz 2024-05-13 11:39 131K wgEncodeGencodeTranscriptSupportV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodeAnnotationRemarkV46.txt.gz 2024-05-13 11:39 1.0M wgEncodeGencodeAnnotationRemarkV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodePubMedV46.txt.gz 2024-05-13 11:39 1.5M wgEncodeGencodePubMedV46.sql 2024-05-13 11:39 1.4K wgEncodeGencodeGeneSymbolV46.txt.gz 2024-05-13 11:39 1.6M wgEncodeGencodeGeneSymbolV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodeTranscriptSourceV46.txt.gz 2024-05-13 11:39 1.3M wgEncodeGencodeTranscriptSourceV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodePdbV46.txt.gz 2024-05-13 11:39 1.0M wgEncodeGencodePdbV46.sql 2024-05-13 11:39 1.4K wgEncodeGencodeUniProtV46.txt.gz 2024-05-13 11:39 1.3M wgEncodeGencodeUniProtV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodeRefSeqV46.txt.gz 2024-05-13 11:39 934K wgEncodeGencodeRefSeqV46.sql 2024-05-13 11:39 1.5K wgEncodeGencodeGeneSourceV46.txt.gz 2024-05-13 11:39 342K wgEncodeGencodeGeneSourceV46.sql 2024-05-13 11:39 1.4K wgEncodeGencodePolyaV46.txt.gz 2024-05-13 11:37 1.7M wgEncodeGencodePolyaV46.sql 2024-05-13 11:37 2.0K knownGeneOldV45.txt.gz 2024-04-05 22:42 11M knownGeneOldV45.sql 2024-04-05 22:42 2.0K knownToGencodeV46.txt.gz 2024-04-02 13:28 1.4M knownToGencodeV46.sql 2024-04-02 13:28 1.4K kgV45ToKgV46.txt.gz 2024-04-02 13:25 4.0M kgV45ToKgV46.sql 2024-04-02 13:25 1.6K wgEncodeGencodeTranscriptionSupportLevelV45.txt.gz 2024-01-11 13:38 889K wgEncodeGencodeTranscriptionSupportLevelV45.sql 2024-01-11 13:38 1.5K wgEncodeGencodeExonSupportV45.txt.gz 2024-01-11 12:43 55M wgEncodeGencodeExonSupportV45.sql 2024-01-11 12:43 1.6K wgEncodeGencodePseudoGeneV45.txt.gz 2024-01-11 12:41 640K wgEncodeGencodePseudoGeneV45.sql 2024-01-11 12:41 2.0K wgEncodeGencodeTagV45.txt.gz 2024-01-11 12:41 2.2M wgEncodeGencodeTagV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodeCompV45.txt.gz 2024-01-11 12:41 10M wgEncodeGencodeCompV45.sql 2024-01-11 12:41 2.0K wgEncodeGencodeAttrsV45.txt.gz 2024-01-11 12:41 7.7M wgEncodeGencodeAttrsV45.sql 2024-01-11 12:41 2.1K wgEncodeGencodeBasicV45.txt.gz 2024-01-11 12:41 5.7M wgEncodeGencodeBasicV45.sql 2024-01-11 12:41 2.0K wgEncodeGencodePdbV45.txt.gz 2024-01-11 12:41 945K wgEncodeGencodePdbV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodeTranscriptSupportV45.txt.gz 2024-01-11 12:41 107K wgEncodeGencodeTranscriptSupportV45.sql 2024-01-11 12:41 1.5K wgEncodeGencodePubMedV45.txt.gz 2024-01-11 12:41 1.5M wgEncodeGencodePubMedV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodeUniProtV45.txt.gz 2024-01-11 12:41 1.3M wgEncodeGencodeUniProtV45.sql 2024-01-11 12:41 1.5K wgEncodeGencodeTranscriptSourceV45.txt.gz 2024-01-11 12:41 1.3M wgEncodeGencodeTranscriptSourceV45.sql 2024-01-11 12:41 1.5K wgEncodeGencodeEntrezGeneV45.txt.gz 2024-01-11 12:41 1.2M wgEncodeGencodeEntrezGeneV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodeAnnotationRemarkV45.txt.gz 2024-01-11 12:41 968K wgEncodeGencodeAnnotationRemarkV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodeRefSeqV45.txt.gz 2024-01-11 12:41 918K wgEncodeGencodeRefSeqV45.sql 2024-01-11 12:41 1.5K wgEncodeGencodeGeneSymbolV45.txt.gz 2024-01-11 12:41 1.6M wgEncodeGencodeGeneSymbolV45.sql 2024-01-11 12:41 1.5K wgEncodeGencodeGeneSourceV45.txt.gz 2024-01-11 12:41 342K wgEncodeGencodeGeneSourceV45.sql 2024-01-11 12:41 1.4K wgEncodeGencodePolyaV45.txt.gz 2024-01-11 12:38 1.7M wgEncodeGencodePolyaV45.sql 2024-01-11 12:38 2.0K extFile.txt.gz 2024-01-08 15:33 28K extFile.sql 2024-01-08 15:33 1.4K gnomadExomesV4.txt.gz 2023-11-16 09:20 229 gnomadExomesV4.sql 2023-11-16 09:20 1.4K gnomadGenomesV4.txt.gz 2023-11-16 09:20 229 gnomadGenomesV4.sql 2023-11-16 09:20 1.4K 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