This directory contains a dump of the UCSC genome annotation database for the Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly of the D. melanogaster genome (dm6, The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics) . 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/47 http://www.ncbi.nlm.nih.gov/assembly/202931 http://www.ncbi.nlm.nih.gov/bioproject/164 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=dm6 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/dm6/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/dm6/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6/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 dm6 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql dm6 --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 2024-11-17 03:37 112 bigFiles.sql 2024-11-17 03:37 1.4K tableList.txt.gz 2024-11-17 03:37 15K tableList.sql 2024-11-17 03:37 1.6K tableDescriptions.txt.gz 2024-11-16 02:03 13K tableDescriptions.sql 2024-11-16 02:03 1.4K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K hgFindSpec.sql 2024-07-25 09:34 1.8K trackDb.txt.gz 2024-07-25 09:34 116K trackDb.sql 2024-07-25 09:34 2.1K refGenePfam.txt.gz 2022-10-14 14:40 551K refGenePfam.sql 2022-10-14 14:40 1.8K mmBlastTab.txt.gz 2022-07-12 17:09 154K mmBlastTab.sql 2022-07-12 17:09 1.7K hgBlastTab.txt.gz 2022-07-12 17:02 154K hgBlastTab.sql 2022-07-12 17:02 1.7K ensPep.txt.gz 2021-05-25 14:33 7.7M ensPep.sql 2021-05-25 14:33 1.3K ensemblSource.txt.gz 2021-05-25 14:33 114K ensemblSource.sql 2021-05-25 14:33 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:29 205K ensemblToGeneName.sql 2021-05-25 14:29 1.4K ensGtp.txt.gz 2021-05-25 14:29 337K ensGtp.sql 2021-05-25 14:29 1.4K ensGene.txt.gz 2021-05-25 14:29 1.4M ensGene.sql 2021-05-25 14:29 1.9K seqNcbiRefSeq.txt.gz 2021-02-11 15:39 521K seqNcbiRefSeq.sql 2021-02-11 15:39 1.6K ncbiRefSeqPepTable.txt.gz 2021-02-11 15:39 8.6M ncbiRefSeqPepTable.sql 2021-02-11 15:39 1.4K ncbiRefSeqOther.txt.gz 2021-02-11 15:39 71 ncbiRefSeqOther.sql 2021-02-11 15:39 1.3K ncbiRefSeqCds.txt.gz 2021-02-11 15:39 214K ncbiRefSeqCds.sql 2021-02-11 15:39 1.4K extNcbiRefSeq.txt.gz 2021-02-11 15:39 86 extNcbiRefSeq.sql 2021-02-11 15:39 1.5K ncbiRefSeqPsl.txt.gz 2021-02-11 14:22 1.6M ncbiRefSeqPsl.sql 2021-02-11 14:22 2.1K ncbiRefSeqLink.txt.gz 2021-02-11 14:22 2.0M ncbiRefSeqLink.sql 2021-02-11 14:22 2.0K ncbiRefSeqCurated.txt.gz 2021-02-11 14:22 1.3M ncbiRefSeqCurated.sql 2021-02-11 14:22 2.0K ncbiRefSeq.txt.gz 2021-02-11 14:22 1.3M ncbiRefSeq.sql 2021-02-11 14:22 1.9K gbLoaded.txt.gz 2020-08-19 00:21 57K gbLoaded.sql 2020-08-19 00:21 1.6K xenoRefSeqAli.txt.gz 2020-08-19 00:20 2.6M xenoRefSeqAli.sql 2020-08-19 00:20 2.1K refSeqAli.txt.gz 2020-08-19 00:20 1.6M refSeqAli.sql 2020-08-19 00:20 2.1K mrnaOrientInfo.txt.gz 2020-08-19 00:15 1.6M mrnaOrientInfo.sql 2020-08-19 00:15 1.8K xenoRefFlat.txt.gz 2020-08-19 00:15 2.4M xenoRefFlat.sql 2020-08-19 00:15 1.7K xenoRefGene.txt.gz 2020-08-19 00:08 2.7M xenoRefGene.sql 2020-08-19 00:08 1.9K refFlat.txt.gz 2020-08-19 00:08 1.7M refFlat.sql 2020-08-19 00:08 1.7K refGene.txt.gz 2020-08-19 00:08 1.9M refGene.sql 2020-08-19 00:08 1.9K xenoMrna.txt.gz 2020-08-18 23:53 57M xenoMrna.sql 2020-08-18 23:53 2.1K all_mrna.txt.gz 2020-08-18 23:53 3.9M all_mrna.sql 2020-08-18 23:53 2.1K phyloP124way.txt.gz 2019-01-20 08:22 3.7M phyloP124way.sql 2019-01-20 08:22 1.8K phastConsElements124way.txt.gz 2019-01-20 08:22 35M phastConsElements124way.sql 2019-01-20 08:22 1.6K phastCons124way.txt.gz 2019-01-20 08:22 3.0M phastCons124way.sql 2019-01-20 08:22 1.8K netTriCas2.txt.gz 2019-01-20 08:22 1.7M netTriCas2.sql 2019-01-20 08:22 2.1K netMusDom2.txt.gz 2019-01-20 08:22 1.8M netMusDom2.sql 2019-01-20 08:22 2.1K netDroYak3.txt.gz 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chainZeugodacus_cucurbitae.txt.gz 2019-01-20 08:21 2.4M chainZeugodacus_cucurbitae.sql 2019-01-20 08:21 1.8K chainZaprionus_indianusLink.txt.gz 2019-01-20 08:21 22M chainZaprionus_indianusLink.sql 2019-01-20 08:21 1.6K chainZaprionus_indianus.txt.gz 2019-01-20 08:21 2.9M chainZaprionus_indianus.sql 2019-01-20 08:21 1.7K chainTrupanea_jonesiLink.txt.gz 2019-01-20 08:21 3.8M chainTrupanea_jonesiLink.sql 2019-01-20 08:21 1.6K chainTrupanea_jonesi.txt.gz 2019-01-20 08:21 967K chainTrupanea_jonesi.sql 2019-01-20 08:21 1.7K chainTrichoceridae_BV_2014Link.txt.gz 2019-01-20 08:21 1.7M chainTrichoceridae_BV_2014Link.sql 2019-01-20 08:21 1.6K chainTrichoceridae_BV_2014.txt.gz 2019-01-20 08:21 492K chainTrichoceridae_BV_2014.sql 2019-01-20 08:21 1.8K chainTriCas2Link.txt.gz 2019-01-20 08:21 12M chainTriCas2Link.sql 2019-01-20 08:21 1.5K chainTriCas2.txt.gz 2019-01-20 08:21 1.6M chainTriCas2.sql 2019-01-20 08:21 1.7K chainTipula_oleraceaLink.txt.gz 2019-01-20 08:21 5.9M chainTipula_oleraceaLink.sql 2019-01-20 08:21 1.6K chainTipula_oleracea.txt.gz 2019-01-20 08:21 1.4M chainTipula_oleracea.sql 2019-01-20 08:21 1.7K chainThemira_minorLink.txt.gz 2019-01-20 08:21 9.8M chainThemira_minorLink.sql 2019-01-20 08:21 1.6K chainThemira_minor.txt.gz 2019-01-20 08:21 1.9M chainThemira_minor.sql 2019-01-20 08:21 1.7K chainTephritis_californicaLink.txt.gz 2019-01-20 08:21 7.0M chainTephritis_californicaLink.sql 2019-01-20 08:21 1.6K chainTephritis_californica.txt.gz 2019-01-20 08:21 1.9M chainTephritis_californica.sql 2019-01-20 08:21 1.8K chainTeleopsis_dalmanniLink.txt.gz 2019-01-20 08:20 58M chainTeleopsis_dalmanniLink.sql 2019-01-20 08:20 1.6K chainTeleopsis_dalmanni.txt.gz 2019-01-20 08:20 5.6M chainTeleopsis_dalmanni.sql 2019-01-20 08:20 1.7K chainStomoxys_calcitransLink.txt.gz 2019-01-20 08:20 15M chainStomoxys_calcitransLink.sql 2019-01-20 08:20 1.6K chainStomoxys_calcitrans.txt.gz 2019-01-20 08:20 2.8M chainStomoxys_calcitrans.sql 2019-01-20 08:20 1.8K chainSphyracephala_brevicornisLink.txt.gz 2019-01-20 08:20 9.0M chainSphyracephala_brevicornisLink.sql 2019-01-20 08:20 1.6K chainSphyracephala_brevicornis.txt.gz 2019-01-20 08:20 1.9M chainSphyracephala_brevicornis.sql 2019-01-20 08:20 1.8K chainScaptodrosophila_lebanonensisLink.txt.gz 2019-01-20 08:20 54M chainScaptodrosophila_lebanonensisLink.sql 2019-01-20 08:20 1.6K chainScaptodrosophila_lebanonensis.txt.gz 2019-01-20 08:20 5.3M chainScaptodrosophila_lebanonensis.sql 2019-01-20 08:20 1.8K chainSarcophagidae_BV_2014Link.txt.gz 2019-01-20 08:20 5.5M chainSarcophagidae_BV_2014Link.sql 2019-01-20 08:20 1.6K chainSarcophagidae_BV_2014.txt.gz 2019-01-20 08:20 1.3M chainSarcophagidae_BV_2014.sql 2019-01-20 08:20 1.8K chainRhagoletis_zephyriaLink.txt.gz 2019-01-20 08:20 58M chainRhagoletis_zephyriaLink.sql 2019-01-20 08:20 1.6K chainRhagoletis_zephyria.txt.gz 2019-01-20 08:19 7.7M chainRhagoletis_zephyria.sql 2019-01-20 08:19 1.8K chainProctacanthus_coquillettiLink.txt.gz 2019-01-20 08:19 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chainPaykullia_maculata.sql 2019-01-20 08:19 1.7K chainNeobellieria_bullataLink.txt.gz 2019-01-20 08:19 9.0M chainNeobellieria_bullataLink.sql 2019-01-20 08:19 1.6K chainNeobellieria_bullata.txt.gz 2019-01-20 08:19 1.9M chainNeobellieria_bullata.sql 2019-01-20 08:19 1.8K chainMusDom2Link.txt.gz 2019-01-20 08:19 20M chainMusDom2Link.sql 2019-01-20 08:19 1.5K chainMusDom2.txt.gz 2019-01-20 08:19 2.9M chainMusDom2.sql 2019-01-20 08:19 1.7K chainMochlonyx_cinctipesLink.txt.gz 2019-01-20 08:19 7.1M chainMochlonyx_cinctipesLink.sql 2019-01-20 08:19 1.6K chainMochlonyx_cinctipes.txt.gz 2019-01-20 08:19 1.5M chainMochlonyx_cinctipes.sql 2019-01-20 08:19 1.8K chainMegaselia_scalarisLink.txt.gz 2019-01-20 08:19 4.3M chainMegaselia_scalarisLink.sql 2019-01-20 08:19 1.6K chainMegaselia_scalaris.txt.gz 2019-01-20 08:19 1.2M chainMegaselia_scalaris.sql 2019-01-20 08:19 1.7K chainMegaselia_abditaLink.txt.gz 2019-01-20 08:19 9.0M chainMegaselia_abditaLink.sql 2019-01-20 08:19 1.6K chainMegaselia_abdita.txt.gz 2019-01-20 08:19 1.8M chainMegaselia_abdita.sql 2019-01-20 08:19 1.7K chainMayetiola_destructorLink.txt.gz 2019-01-20 08:19 5.4M chainMayetiola_destructorLink.sql 2019-01-20 08:19 1.6K chainMayetiola_destructor.txt.gz 2019-01-20 08:19 845K chainMayetiola_destructor.sql 2019-01-20 08:19 1.8K chainLutzomyia_longipalpisLink.txt.gz 2019-01-20 08:19 8.4M chainLutzomyia_longipalpisLink.sql 2019-01-20 08:19 1.6K chainLutzomyia_longipalpis.txt.gz 2019-01-20 08:19 1.5M chainLutzomyia_longipalpis.sql 2019-01-20 08:19 1.8K chainLucilia_sericataLink.txt.gz 2019-01-20 08:19 9.8M chainLucilia_sericataLink.sql 2019-01-20 08:19 1.6K chainLucilia_sericata.txt.gz 2019-01-20 08:19 1.9M chainLucilia_sericata.sql 2019-01-20 08:19 1.7K chainLucilia_cuprinaLink.txt.gz 2019-01-20 08:19 19M chainLucilia_cuprinaLink.sql 2019-01-20 08:19 1.6K chainLucilia_cuprina.txt.gz 2019-01-20 08:19 2.5M chainLucilia_cuprina.sql 2019-01-20 08:19 1.7K chainLiriomyza_trifoliiLink.txt.gz 2019-01-20 08:19 4.6M chainLiriomyza_trifoliiLink.sql 2019-01-20 08:19 1.6K chainLiriomyza_trifolii.txt.gz 2019-01-20 08:19 942K chainLiriomyza_trifolii.sql 2019-01-20 08:19 1.7K chainHolcocephala_fuscaLink.txt.gz 2019-01-20 08:19 7.0M chainHolcocephala_fuscaLink.sql 2019-01-20 08:19 1.6K chainHolcocephala_fusca.txt.gz 2019-01-20 08:19 1.5M chainHolcocephala_fusca.sql 2019-01-20 08:19 1.7K chainHermetia_illucensLink.txt.gz 2019-01-20 08:18 7.4M chainHermetia_illucensLink.sql 2019-01-20 08:18 1.6K chainHermetia_illucens.txt.gz 2019-01-20 08:18 2.1M chainHermetia_illucens.sql 2019-01-20 08:18 1.7K chainHaematobia_irritansLink.txt.gz 2019-01-20 08:18 11M chainHaematobia_irritansLink.sql 2019-01-20 08:18 1.6K chainHaematobia_irritans.txt.gz 2019-01-20 08:18 2.0M chainHaematobia_irritans.sql 2019-01-20 08:18 1.8K chainGlossina_palpalis_gambiensisLink.txt.gz 2019-01-20 08:18 10M chainGlossina_palpalis_gambiensisLink.sql 2019-01-20 08:18 1.6K chainGlossina_palpalis_gambiensis.txt.gz 2019-01-20 08:18 1.5M chainGlossina_palpalis_gambiensis.sql 2019-01-20 08:18 1.8K chainGlossina_pallidipesLink.txt.gz 2019-01-20 08:18 10M chainGlossina_pallidipesLink.sql 2019-01-20 08:18 1.6K chainGlossina_pallidipes.txt.gz 2019-01-20 08:18 1.5M chainGlossina_pallidipes.sql 2019-01-20 08:18 1.8K chainGlossina_morsitans_2Link.txt.gz 2019-01-20 08:18 10M chainGlossina_morsitans_2Link.sql 2019-01-20 08:18 1.6K chainGlossina_morsitans_2.txt.gz 2019-01-20 08:18 1.6M chainGlossina_morsitans_2.sql 2019-01-20 08:18 1.8K chainGlossina_morsitans_1Link.txt.gz 2019-01-20 08:18 8.1M chainGlossina_morsitans_1Link.sql 2019-01-20 08:18 1.6K chainGlossina_morsitans_1.txt.gz 2019-01-20 08:18 1.5M chainGlossina_morsitans_1.sql 2019-01-20 08:18 1.8K chainGlossina_fuscipesLink.txt.gz 2019-01-20 08:18 10M chainGlossina_fuscipesLink.sql 2019-01-20 08:18 1.6K chainGlossina_fuscipes.txt.gz 2019-01-20 08:18 1.5M chainGlossina_fuscipes.sql 2019-01-20 08:18 1.7K chainGlossina_brevipalpisLink.txt.gz 2019-01-20 08:18 10M 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