This directory contains a dump of the UCSC genome annotation database for the Feb. 2013 (WBcel235/ce11) assembly of the C. elegans genome (ce11, C. elegans Sequencing Consortium WBcel235). 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/41 http://www.ncbi.nlm.nih.gov/genome/assembly/554278 http://www.ncbi.nlm.nih.gov/bioproject/13758 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=ce11 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/ce11/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/ce11/database/ . For a single file, e.g. gc5BaseBw.txt.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/gc5BaseBw.txt.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce11/database/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/ce11/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 ce11 < chromInfo.sql ## load data from the txt.gz file $ zcat chromInfo.txt.gz | hgsql ce11 --local-infile=1 -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;' The C. elegans sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of these data are properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html for credit information. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome (that is, 30 Mb or more). 4. Any redistribution of the data should carry this notice. ----------------------------------------------------------------------------- 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 14:25 1.5M xenoRefSeqAli.sql 2020-08-18 14:25 2.1K xenoRefGene.txt.gz 2020-08-18 14:25 1.7M xenoRefGene.sql 2020-08-18 14:25 2.0K xenoRefFlat.txt.gz 2020-08-18 14:25 1.5M xenoRefFlat.sql 2020-08-18 14:25 1.7K xenoMrna.txt.gz 2020-08-18 14:04 33M xenoMrna.sql 2020-08-18 14:04 2.1K ws245GenesPeptide.txt.gz 2016-03-18 11:18 4.5M ws245GenesPeptide.sql 2016-03-18 11:18 1.4K ws245Genes.txt.gz 2016-03-18 11:17 2.2M ws245Genes.sql 2016-03-18 11:17 1.9K windowmaskerSdust.txt.gz 2016-03-18 11:17 7.2M windowmaskerSdust.sql 2016-03-18 11:17 1.5K ucscToRefSeq.txt.gz 2018-02-18 05:46 141 ucscToRefSeq.sql 2018-02-18 05:46 1.4K ucscToINSDC.txt.gz 2016-03-18 11:17 136 ucscToINSDC.sql 2016-03-18 11:17 1.4K trackDb.txt.gz 2023-12-05 13:52 72K trackDb.sql 2023-12-05 13:52 2.1K tableList.txt.gz 2024-12-01 03:29 16K tableList.sql 2024-12-01 03:29 1.6K tableDescriptions.txt.gz 2024-11-30 02:03 13K tableDescriptions.sql 2024-11-30 02:03 1.5K simpleRepeat.txt.gz 2016-03-18 11:17 1.2M simpleRepeat.sql 2016-03-18 11:17 1.9K seqNcbiRefSeq.txt.gz 2020-07-02 16:49 674K seqNcbiRefSeq.sql 2020-07-02 16:49 1.6K rmsk.txt.gz 2016-03-18 11:17 2.1M rmsk.sql 2016-03-18 11:17 1.9K refSeqAli.txt.gz 2020-08-18 14:25 2.6M refSeqAli.sql 2020-08-18 14:25 2.1K refGene.txt.gz 2020-08-18 14:25 2.3M refGene.sql 2020-08-18 14:25 1.9K refFlat.txt.gz 2020-08-18 14:25 2.1M refFlat.sql 2020-08-18 14:25 1.7K phyloP135way.txt.gz 2019-01-13 04:04 3.0M phyloP135way.sql 2019-01-13 04:04 1.8K phyloP26way.txt.gz 2016-03-18 11:17 2.7M phyloP26way.sql 2016-03-18 11:17 1.8K phastConsElements135way.txt.gz 2019-01-13 04:04 19M phastConsElements135way.sql 2019-01-13 04:04 1.6K phastConsElements26way.txt.gz 2016-03-18 11:17 4.0M phastConsElements26way.sql 2016-03-18 11:17 1.6K phastCons135way.txt.gz 2019-01-13 04:04 2.5M phastCons135way.sql 2019-01-13 04:04 1.8K phastCons26way.txt.gz 2016-03-18 11:17 2.4M phastCons26way.sql 2016-03-18 11:17 1.8K netTriSui1.txt.gz 2019-01-13 04:04 322K netTriSui1.sql 2019-01-13 04:04 2.1K netTriSpi1.txt.gz 2019-01-13 04:04 312K netTriSpi1.sql 2019-01-13 04:04 2.1K netStrRat2.txt.gz 2019-01-13 04:04 2.6M netStrRat2.sql 2019-01-13 04:04 2.1K netPriPac3.txt.gz 2019-01-13 04:04 781K netPriPac3.sql 2019-01-13 04:04 2.1K netPriExs1.txt.gz 2019-01-13 04:04 766K netPriExs1.sql 2019-01-13 04:04 2.1K netPanRed1.txt.gz 2019-01-13 04:04 692K netPanRed1.sql 2019-01-13 04:04 2.1K netOncVol1.txt.gz 2019-01-13 04:04 634K netOncVol1.sql 2019-01-13 04:04 2.1K netNecAme1.txt.gz 2019-01-13 04:04 1.0M netNecAme1.sql 2019-01-13 04:04 2.1K netMelInc2.txt.gz 2019-01-13 04:04 386K netMelInc2.sql 2019-01-13 04:04 2.1K netMelHap1.txt.gz 2019-01-13 04:04 429K netMelHap1.sql 2019-01-13 04:04 2.1K netLoaLoa1.txt.gz 2019-01-13 04:04 606K netLoaLoa1.sql 2019-01-13 04:04 2.1K netHetBac1.txt.gz 2019-01-13 04:04 1.0M netHetBac1.sql 2019-01-13 04:04 2.1K netHaeCon2.txt.gz 2019-01-13 04:04 1.0M netHaeCon2.sql 2019-01-13 04:04 2.1K netDirImm1.txt.gz 2019-01-13 04:04 598K netDirImm1.sql 2019-01-13 04:04 2.1K netCi3.txt.gz 2017-06-13 16:11 294K netCi3.sql 2017-06-13 16:11 2.1K netCb4.txt.gz 2019-01-13 03:53 3.3M netCb4.sql 2019-01-13 03:53 2.1K netCaeSp111.txt.gz 2019-01-13 04:04 4.1M netCaeSp111.sql 2019-01-13 04:04 2.1K netCaeSp51.txt.gz 2019-01-13 04:04 3.4M netCaeSp51.sql 2019-01-13 04:04 2.1K netCaeRem4.txt.gz 2019-01-13 04:04 4.2M netCaeRem4.sql 2019-01-13 04:04 2.1K netCaePb3.txt.gz 2019-01-13 03:52 4.1M netCaePb3.sql 2019-01-13 03:52 2.1K netCaeJap4.txt.gz 2019-01-13 04:04 3.6M netCaeJap4.sql 2019-01-13 04:04 2.1K netCaeAng2.txt.gz 2019-01-13 04:04 3.6M netCaeAng2.sql 2019-01-13 04:04 2.1K netBurXyl1.txt.gz 2019-01-13 04:04 694K netBurXyl1.sql 2019-01-13 04:04 2.1K netBruMal2.txt.gz 2019-01-13 04:04 624K netBruMal2.sql 2019-01-13 04:04 2.1K netAscSuu1.txt.gz 2019-01-13 04:04 792K netAscSuu1.sql 2019-01-13 04:04 2.1K netAncCey1.txt.gz 2019-01-13 04:04 1.5M netAncCey1.sql 2019-01-13 04:04 2.1K nestedRepeats.txt.gz 2016-03-18 11:16 113K nestedRepeats.sql 2016-03-18 11:16 1.9K ncbiRefSeqPsl.txt.gz 2020-07-02 15:50 2.4M ncbiRefSeqPsl.sql 2020-07-02 15:50 2.1K ncbiRefSeqPepTable.txt.gz 2020-07-02 16:38 6.1M ncbiRefSeqPepTable.sql 2020-07-02 16:38 1.4K ncbiRefSeqOther.txt.gz 2020-07-02 16:38 72 ncbiRefSeqOther.sql 2020-07-02 16:38 1.3K ncbiRefSeqLink.txt.gz 2020-07-02 15:50 1.3M ncbiRefSeqLink.sql 2020-07-02 15:50 2.0K ncbiRefSeqCurated.txt.gz 2020-07-02 15:50 2.2M ncbiRefSeqCurated.sql 2020-07-02 15:50 2.0K ncbiRefSeqCds.txt.gz 2020-07-02 16:38 183K ncbiRefSeqCds.sql 2020-07-02 16:38 1.4K ncbiRefSeq.txt.gz 2020-07-02 15:50 2.2M ncbiRefSeq.sql 2020-07-02 15:50 1.9K multiz135waySummary.txt.gz 2019-01-13 04:04 24M multiz135waySummary.sql 2019-01-13 04:04 1.6K multiz135wayFrames.txt.gz 2019-01-13 04:04 39M multiz135wayFrames.sql 2019-01-13 04:04 1.7K multiz135way.txt.gz 2019-01-13 04:03 87M multiz135way.sql 2019-01-13 04:03 1.5K multiz26waySummary.txt.gz 2016-03-18 11:17 4.7M multiz26waySummary.sql 2016-03-18 11:17 1.6K multiz26wayFrames.txt.gz 2016-03-18 11:13 23M multiz26wayFrames.sql 2016-03-18 11:13 1.7K multiz26way.txt.gz 2016-03-18 11:13 20M multiz26way.sql 2016-03-18 11:13 1.5K mrnaOrientInfo.txt.gz 2020-08-18 14:25 825K mrnaOrientInfo.sql 2020-08-18 14:25 1.8K mmBlastTab.txt.gz 2022-07-12 17:09 122K mmBlastTab.sql 2022-07-12 17:09 1.7K locusName.txt.gz 2018-06-10 06:29 2.6M locusName.sql 2018-06-10 06:29 1.5K intronEst.txt.gz 2016-06-05 09:17 11M intronEst.sql 2016-06-05 09:17 2.1K history.txt.gz 2016-03-18 11:12 2.2K history.sql 2016-03-18 11:12 1.6K hgFindSpec.txt.gz 2023-12-05 13:52 1.2K hgFindSpec.sql 2023-12-05 13:52 1.8K hgBlastTab.txt.gz 2022-07-12 17:02 117K hgBlastTab.sql 2022-07-12 17:02 1.7K grp.txt.gz 2016-03-18 11:13 213 grp.sql 2016-03-18 11:13 1.3K gold.txt.gz 2016-03-18 11:13 55K gold.sql 2016-03-18 11:13 1.7K genscan.txt.gz 2016-03-18 11:13 678K genscan.sql 2016-03-18 11:13 1.7K gc5BaseBw.txt.gz 2016-03-18 11:13 63 gc5BaseBw.sql 2016-03-18 11:13 1.3K gbLoaded.txt.gz 2020-08-18 14:30 46K gbLoaded.sql 2020-08-18 14:30 1.6K gap.txt.gz 2016-03-18 11:13 28 gap.sql 2016-03-18 11:13 1.6K extNcbiRefSeq.txt.gz 2020-07-02 16:38 87 extNcbiRefSeq.sql 2020-07-02 16:38 1.5K extFile.txt.gz 2019-01-13 03:52 256 extFile.sql 2019-01-13 03:52 1.4K estOrientInfo.txt.gz 2016-06-05 09:17 4.0M estOrientInfo.sql 2016-06-05 09:17 1.8K ensemblToGeneName.txt.gz 2021-05-25 14:23 312K ensemblToGeneName.sql 2021-05-25 14:23 1.4K ensemblSource.txt.gz 2021-05-25 14:25 186K ensemblSource.sql 2021-05-25 14:25 1.4K ensPep.txt.gz 2021-05-25 14:25 5.0M ensPep.sql 2021-05-25 14:25 1.3K ensGtp.txt.gz 2021-05-25 14:23 384K ensGtp.sql 2021-05-25 14:23 1.4K ensGene.txt.gz 2021-05-25 14:23 2.3M ensGene.sql 2021-05-25 14:23 1.9K cytoBandIdeo.txt.gz 2016-03-18 11:13 118 cytoBandIdeo.sql 2016-03-18 11:13 1.5K crisprTargets.txt.gz 2018-06-10 06:29 60 crisprTargets.sql 2018-06-10 06:29 1.3K crisprRanges.txt.gz 2018-06-10 06:29 325K crisprRanges.sql 2018-06-10 06:29 1.4K cpgIslandExtUnmasked.txt.gz 2016-03-18 11:13 74K cpgIslandExtUnmasked.sql 2016-03-18 11:13 1.7K cpgIslandExt.txt.gz 2016-03-18 11:13 62K cpgIslandExt.sql 2016-03-18 11:13 1.7K chromInfo.txt.gz 2016-03-18 11:13 124 chromInfo.sql 2016-03-18 11:13 1.4K chromAlias.txt.gz 2018-02-18 05:46 151 chromAlias.sql 2018-02-18 05:46 1.4K chainWuchereria_bancroftiLink.txt.gz 2019-01-13 04:03 15M chainWuchereria_bancroftiLink.sql 2019-01-13 04:03 1.6K chainWuchereria_bancrofti.txt.gz 2019-01-13 04:03 1.6M chainWuchereria_bancrofti.sql 2019-01-13 04:03 1.8K chainTrichuris_trichiuraLink.txt.gz 2019-01-13 04:03 3.6M chainTrichuris_trichiuraLink.sql 2019-01-13 04:03 1.6K chainTrichuris_trichiura.txt.gz 2019-01-13 04:03 947K chainTrichuris_trichiura.sql 2019-01-13 04:03 1.8K chainTrichuris_murisLink.txt.gz 2019-01-13 04:03 2.7M chainTrichuris_murisLink.sql 2019-01-13 04:03 1.6K chainTrichuris_muris.txt.gz 2019-01-13 04:03 633K chainTrichuris_muris.sql 2019-01-13 04:03 1.7K chainTrichinella_zimbabwensisLink.txt.gz 2019-01-13 04:03 6.7M chainTrichinella_zimbabwensisLink.sql 2019-01-13 04:03 1.6K chainTrichinella_zimbabwensis.txt.gz 2019-01-13 04:03 712K chainTrichinella_zimbabwensis.sql 2019-01-13 04:03 1.8K chainTrichinella_spiralisLink.txt.gz 2019-01-13 04:03 6.3M chainTrichinella_spiralisLink.sql 2019-01-13 04:03 1.6K chainTrichinella_spiralis.txt.gz 2019-01-13 04:03 748K chainTrichinella_spiralis.sql 2019-01-13 04:03 1.8K chainTrichinella_pseudospiralisLink.txt.gz 2019-01-13 04:03 6.3M chainTrichinella_pseudospiralisLink.sql 2019-01-13 04:03 1.6K chainTrichinella_pseudospiralis.txt.gz 2019-01-13 04:03 681K chainTrichinella_pseudospiralis.sql 2019-01-13 04:03 1.8K chainTrichinella_patagoniensisLink.txt.gz 2019-01-13 04:03 5.9M chainTrichinella_patagoniensisLink.sql 2019-01-13 04:03 1.6K chainTrichinella_patagoniensis.txt.gz 2019-01-13 04:03 680K chainTrichinella_patagoniensis.sql 2019-01-13 04:03 1.8K chainTrichinella_papuaeLink.txt.gz 2019-01-13 04:03 6.4M chainTrichinella_papuaeLink.sql 2019-01-13 04:03 1.6K chainTrichinella_papuae.txt.gz 2019-01-13 04:03 681K chainTrichinella_papuae.sql 2019-01-13 04:03 1.7K chainTrichinella_nelsoniLink.txt.gz 2019-01-13 04:03 5.8M chainTrichinella_nelsoniLink.sql 2019-01-13 04:03 1.6K chainTrichinella_nelsoni.txt.gz 2019-01-13 04:03 662K chainTrichinella_nelsoni.sql 2019-01-13 04:03 1.8K chainTrichinella_nativaLink.txt.gz 2019-01-13 04:03 5.7M chainTrichinella_nativaLink.sql 2019-01-13 04:03 1.6K chainTrichinella_nativa.txt.gz 2019-01-13 04:03 653K chainTrichinella_nativa.sql 2019-01-13 04:03 1.7K chainTrichinella_murrelliLink.txt.gz 2019-01-13 04:03 6.9M chainTrichinella_murrelliLink.sql 2019-01-13 04:03 1.6K chainTrichinella_murrelli.txt.gz 2019-01-13 04:03 718K chainTrichinella_murrelli.sql 2019-01-13 04:03 1.8K chainTrichinella_britoviLink.txt.gz 2019-01-13 04:03 5.9M chainTrichinella_britoviLink.sql 2019-01-13 04:03 1.6K chainTrichinella_britovi.txt.gz 2019-01-13 04:03 660K chainTrichinella_britovi.sql 2019-01-13 04:03 1.8K chainTrichinella_T9Link.txt.gz 2019-01-13 04:03 5.9M chainTrichinella_T9Link.sql 2019-01-13 04:03 1.6K chainTrichinella_T9.txt.gz 2019-01-13 04:03 668K chainTrichinella_T9.sql 2019-01-13 04:03 1.7K chainTrichinella_T8Link.txt.gz 2019-01-13 04:03 5.9M chainTrichinella_T8Link.sql 2019-01-13 04:03 1.6K chainTrichinella_T8.txt.gz 2019-01-13 04:03 655K chainTrichinella_T8.sql 2019-01-13 04:03 1.7K chainTrichinella_T6Link.txt.gz 2019-01-13 04:03 6.0M chainTrichinella_T6Link.sql 2019-01-13 04:03 1.6K chainTrichinella_T6.txt.gz 2019-01-13 04:03 671K chainTrichinella_T6.sql 2019-01-13 04:03 1.7K chainTriSui1Link.txt.gz 2019-01-13 04:03 972K chainTriSui1Link.sql 2019-01-13 04:03 1.5K chainTriSui1.txt.gz 2019-01-13 04:03 348K chainTriSui1.sql 2019-01-13 04:03 1.7K chainTriSpi1Link.txt.gz 2019-01-13 04:03 927K chainTriSpi1Link.sql 2019-01-13 04:03 1.5K chainTriSpi1.txt.gz 2019-01-13 04:03 239K chainTriSpi1.sql 2019-01-13 04:03 1.7K chainToxocara_canisLink.txt.gz 2019-01-13 04:03 9.7M chainToxocara_canisLink.sql 2019-01-13 04:03 1.6K chainToxocara_canis.txt.gz 2019-01-13 04:03 3.2M chainToxocara_canis.sql 2019-01-13 04:03 1.7K chainTeladorsagia_circumcinctaLink.txt.gz 2019-01-13 04:03 18M chainTeladorsagia_circumcinctaLink.sql 2019-01-13 04:03 1.6K chainTeladorsagia_circumcincta.txt.gz 2019-01-13 04:03 6.4M chainTeladorsagia_circumcincta.sql 2019-01-13 04:03 1.8K chainTaenia_soliumLink.txt.gz 2019-01-13 04:03 1.9M chainTaenia_soliumLink.sql 2019-01-13 04:03 1.6K chainTaenia_solium.txt.gz 2019-01-13 04:03 518K chainTaenia_solium.sql 2019-01-13 04:03 1.7K chainTaenia_saginataLink.txt.gz 2019-01-13 04:03 2.3M chainTaenia_saginataLink.sql 2019-01-13 04:03 1.6K chainTaenia_saginata.txt.gz 2019-01-13 04:03 643K chainTaenia_saginata.sql 2019-01-13 04:03 1.7K chainTaenia_multicepsLink.txt.gz 2019-01-13 04:03 3.1M chainTaenia_multicepsLink.sql 2019-01-13 04:03 1.6K chainTaenia_multiceps.txt.gz 2019-01-13 04:03 739K chainTaenia_multiceps.sql 2019-01-13 04:03 1.7K chainTaenia_asiaticaLink.txt.gz 2019-01-13 04:02 2.2M chainTaenia_asiaticaLink.sql 2019-01-13 04:02 1.6K chainTaenia_asiatica.txt.gz 2019-01-13 04:02 635K chainTaenia_asiatica.sql 2019-01-13 04:02 1.7K chainSubanguina_moxaeLink.txt.gz 2019-01-13 04:02 7.1M chainSubanguina_moxaeLink.sql 2019-01-13 04:02 1.6K chainSubanguina_moxae.txt.gz 2019-01-13 04:02 1.7M chainSubanguina_moxae.sql 2019-01-13 04:02 1.7K chainStrongyloides_venezuelensisLink.txt.gz 2019-01-13 04:02 48M chainStrongyloides_venezuelensisLink.sql 2019-01-13 04:02 1.6K chainStrongyloides_venezuelensis.txt.gz 2019-01-13 04:02 4.3M chainStrongyloides_venezuelensis.sql 2019-01-13 04:02 1.8K chainStrongyloides_stercoralisLink.txt.gz 2019-01-13 04:02 54M chainStrongyloides_stercoralisLink.sql 2019-01-13 04:02 1.6K chainStrongyloides_stercoralis.txt.gz 2019-01-13 04:02 5.2M chainStrongyloides_stercoralis.sql 2019-01-13 04:02 1.8K chainStrongyloides_papillosusLink.txt.gz 2019-01-13 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