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 - all_est.sql 2016-06-05 09:17 2.1K all_est.txt.gz 2016-06-05 09:17 14M all_mrna.sql 2020-08-18 14:04 2.1K all_mrna.txt.gz 2020-08-18 14:04 317K augustusGene.sql 2016-03-18 11:12 1.9K augustusGene.txt.gz 2016-03-18 11:12 1.3M bigFiles.sql 2024-09-29 03:29 1.4K bigFiles.txt.gz 2024-09-29 03:29 113 chainAcrobeloides_nanus.sql 2019-01-13 03:52 1.7K chainAcrobeloides_nanus.txt.gz 2019-01-13 03:52 4.4M chainAcrobeloides_nanusLink.sql 2019-01-13 03:52 1.6K chainAcrobeloides_nanusLink.txt.gz 2019-01-13 03:52 27M chainAncCey1.sql 2019-01-13 03:52 1.7K chainAncCey1.txt.gz 2019-01-13 03:52 4.6M chainAncCey1Link.sql 2019-01-13 03:52 1.5K chainAncCey1Link.txt.gz 2019-01-13 03:52 15M chainAncylostoma_caninum.sql 2019-01-13 03:52 1.8K chainAncylostoma_caninum.txt.gz 2019-01-13 03:52 4.9M chainAncylostoma_caninumLink.sql 2019-01-13 03:52 1.6K chainAncylostoma_caninumLink.txt.gz 2019-01-13 03:52 16M chainAncylostoma_duodenale.sql 2019-01-13 03:52 1.8K chainAncylostoma_duodenale.txt.gz 2019-01-13 03:52 4.8M chainAncylostoma_duodenaleLink.sql 2019-01-13 03:52 1.6K chainAncylostoma_duodenaleLink.txt.gz 2019-01-13 03:52 15M chainAngiostrongylus_cantonensis.sql 2019-01-13 03:53 1.8K chainAngiostrongylus_cantonensis.txt.gz 2019-01-13 03:53 2.7M chainAngiostrongylus_cantonensisLink.sql 2019-01-13 03:52 1.6K chainAngiostrongylus_cantonensisLink.txt.gz 2019-01-13 03:52 6.7M chainAscSuu1.sql 2019-01-13 03:52 1.7K chainAscSuu1.txt.gz 2019-01-13 03:52 706K chainAscSuu1Link.sql 2019-01-13 03:52 1.5K chainAscSuu1Link.txt.gz 2019-01-13 03:52 1.8M chainAscaris_suum.sql 2019-01-13 03:53 1.7K chainAscaris_suum.txt.gz 2019-01-13 03:53 2.7M chainAscaris_suumLink.sql 2019-01-13 03:52 1.6K chainAscaris_suumLink.txt.gz 2019-01-13 03:52 10M chainBruMal2.sql 2019-01-13 03:52 1.7K chainBruMal2.txt.gz 2019-01-13 03:52 418K chainBruMal2Link.sql 2019-01-13 03:52 1.5K chainBruMal2Link.txt.gz 2019-01-13 03:52 1.5M chainBrugia_malayi.sql 2019-01-13 03:52 1.7K chainBrugia_malayi.txt.gz 2019-01-13 03:52 1.9M chainBrugia_malayiLink.sql 2019-01-13 03:53 1.6K chainBrugia_malayiLink.txt.gz 2019-01-13 03:53 12M chainBrugia_pahangi.sql 2019-01-13 03:53 1.7K chainBrugia_pahangi.txt.gz 2019-01-13 03:53 1.6M chainBrugia_pahangiLink.sql 2019-01-13 03:53 1.6K chainBrugia_pahangiLink.txt.gz 2019-01-13 03:53 14M chainBurXyl1.sql 2019-01-13 03:53 1.7K chainBurXyl1.txt.gz 2019-01-13 03:53 800K chainBurXyl1Link.sql 2019-01-13 03:53 1.5K chainBurXyl1Link.txt.gz 2019-01-13 03:53 2.7M chainBursaphelenchus_xylophilus.sql 2019-01-13 03:53 1.8K chainBursaphelenchus_xylophilus.txt.gz 2019-01-13 03:53 3.6M chainBursaphelenchus_xylophilusLink.sql 2019-01-13 03:53 1.6K chainBursaphelenchus_xylophilusLink.txt.gz 2019-01-13 03:53 13M chainC_briggsae.sql 2019-01-13 03:53 1.7K chainC_briggsae.txt.gz 2019-01-13 03:53 9.2M chainC_briggsaeLink.sql 2019-01-13 03:53 1.6K chainC_briggsaeLink.txt.gz 2019-01-13 03:53 61M chainC_latens.sql 2019-01-13 03:54 1.7K chainC_latens.txt.gz 2019-01-13 03:54 7.3M chainC_latensLink.sql 2019-01-13 03:54 1.5K chainC_latensLink.txt.gz 2019-01-13 03:54 47M chainC_nigoni.sql 2019-01-13 03:54 1.7K chainC_nigoni.txt.gz 2019-01-13 03:54 11M chainC_nigoniLink.sql 2019-01-13 03:54 1.5K chainC_nigoniLink.txt.gz 2019-01-13 03:54 70M chainC_sp21_LS_2015.sql 2019-01-13 03:55 1.7K chainC_sp21_LS_2015.txt.gz 2019-01-13 03:55 3.2M chainC_sp21_LS_2015Link.sql 2019-01-13 03:55 1.6K chainC_sp21_LS_2015Link.txt.gz 2019-01-13 03:55 15M chainC_sp26_LS_2015.sql 2019-01-13 03:55 1.7K chainC_sp26_LS_2015.txt.gz 2019-01-13 03:55 8.5M chainC_sp26_LS_2015Link.sql 2019-01-13 03:55 1.6K chainC_sp26_LS_2015Link.txt.gz 2019-01-13 03:55 52M chainC_sp31_LS_2015.sql 2019-01-13 03:55 1.7K chainC_sp31_LS_2015.txt.gz 2019-01-13 03:55 5.6M chainC_sp31_LS_2015Link.sql 2019-01-13 03:56 1.6K chainC_sp31_LS_2015Link.txt.gz 2019-01-13 03:56 35M chainC_sp32_LS_2015.sql 2019-01-13 03:53 1.7K chainC_sp32_LS_2015.txt.gz 2019-01-13 03:53 6.1M chainC_sp32_LS_2015Link.sql 2019-01-13 03:53 1.6K chainC_sp32_LS_2015Link.txt.gz 2019-01-13 03:53 25M chainC_sp34_TK_2017.sql 2019-01-13 03:53 1.7K chainC_sp34_TK_2017.txt.gz 2019-01-13 03:53 7.0M chainC_sp34_TK_2017Link.sql 2019-01-13 03:55 1.6K chainC_sp34_TK_2017Link.txt.gz 2019-01-13 03:55 39M chainC_sp38_MB_2015.sql 2019-01-13 03:55 1.7K chainC_sp38_MB_2015.txt.gz 2019-01-13 03:55 7.0M chainC_sp38_MB_2015Link.sql 2019-01-13 03:55 1.6K chainC_sp38_MB_2015Link.txt.gz 2019-01-13 03:55 45M chainC_sp39_LS_2015.sql 2019-01-13 03:55 1.7K chainC_sp39_LS_2015.txt.gz 2019-01-13 03:55 7.2M chainC_sp39_LS_2015Link.sql 2019-01-13 03:55 1.6K chainC_sp39_LS_2015Link.txt.gz 2019-01-13 03:55 35M chainC_sp40_LS_2015.sql 2019-01-13 03:56 1.7K chainC_sp40_LS_2015.txt.gz 2019-01-13 03:56 6.9M chainC_sp40_LS_2015Link.sql 2019-01-13 03:53 1.6K chainC_sp40_LS_2015Link.txt.gz 2019-01-13 03:53 40M chainCaeAng2.sql 2019-01-13 03:54 1.7K chainCaeAng2.txt.gz 2019-01-13 03:54 7.5M chainCaeAng2Link.sql 2019-01-13 03:54 1.5K chainCaeAng2Link.txt.gz 2019-01-13 03:54 37M chainCaeJap4.sql 2019-01-13 03:54 1.7K chainCaeJap4.txt.gz 2019-01-13 03:54 8.5M chainCaeJap4Link.sql 2019-01-13 03:54 1.5K chainCaeJap4Link.txt.gz 2019-01-13 03:54 39M chainCaePb3.sql 2019-01-13 03:56 1.7K chainCaePb3.txt.gz 2019-01-13 03:56 10M chainCaePb3Link.sql 2019-01-13 03:56 1.5K chainCaePb3Link.txt.gz 2019-01-13 03:56 64M chainCaeRem4.sql 2019-01-13 03:56 1.7K chainCaeRem4.txt.gz 2019-01-13 03:56 8.5M chainCaeRem4Link.sql 2019-01-13 03:56 1.5K chainCaeRem4Link.txt.gz 2019-01-13 03:56 59M chainCaeSp51.sql 2019-01-13 03:57 1.7K chainCaeSp51.txt.gz 2019-01-13 03:57 3.1M chainCaeSp51Link.sql 2019-01-13 03:57 1.5K chainCaeSp51Link.txt.gz 2019-01-13 03:57 18M chainCaeSp111.sql 2019-01-13 03:56 1.7K chainCaeSp111.txt.gz 2019-01-13 03:56 7.6M chainCaeSp111Link.sql 2019-01-13 03:56 1.5K chainCaeSp111Link.txt.gz 2019-01-13 03:57 47M chainCb4.sql 2019-01-13 03:52 1.7K chainCb4.txt.gz 2019-01-13 03:52 3.0M chainCb4Link.sql 2019-01-13 03:57 1.5K chainCb4Link.txt.gz 2019-01-13 03:57 17M chainCi3.sql 2017-06-13 16:11 1.7K chainCi3.txt.gz 2017-06-13 16:11 331K chainCi3Link.sql 2017-06-13 16:11 1.5K chainCi3Link.txt.gz 2017-06-13 16:11 700K chainClonorchis_sinensis.sql 2019-01-13 03:57 1.8K chainClonorchis_sinensis.txt.gz 2019-01-13 03:57 708K chainClonorchis_sinensisLink.sql 2019-01-13 03:57 1.6K chainClonorchis_sinensisLink.txt.gz 2019-01-13 03:57 2.0M chainDicrocoelium_dendriticum.sql 2019-01-13 03:57 1.8K chainDicrocoelium_dendriticum.txt.gz 2019-01-13 03:57 181K chainDicrocoelium_dendriticumLink.sql 2019-01-13 03:57 1.6K chainDicrocoelium_dendriticumLink.txt.gz 2019-01-13 03:57 326K chainDictyocaulus_viviparus.sql 2019-01-13 03:57 1.8K chainDictyocaulus_viviparus.txt.gz 2019-01-13 03:57 2.5M chainDictyocaulus_viviparusLink.sql 2019-01-13 03:57 1.6K chainDictyocaulus_viviparusLink.txt.gz 2019-01-13 03:57 11M chainDiploscapter_coronatus.sql 2019-01-13 03:57 1.8K chainDiploscapter_coronatus.txt.gz 2019-01-13 03:57 1.7M chainDiploscapter_coronatusLink.sql 2019-01-13 03:57 1.6K chainDiploscapter_coronatusLink.txt.gz 2019-01-13 03:57 19M chainDiploscapter_pachys.sql 2019-01-13 03:57 1.8K chainDiploscapter_pachys.txt.gz 2019-01-13 03:57 1.5M chainDiploscapter_pachysLink.sql 2019-01-13 03:57 1.6K chainDiploscapter_pachysLink.txt.gz 2019-01-13 03:57 16M chainDirImm1.sql 2019-01-13 03:57 1.7K chainDirImm1.txt.gz 2019-01-13 03:57 385K chainDirImm1Link.sql 2019-01-13 03:57 1.5K chainDirImm1Link.txt.gz 2019-01-13 03:57 1.4M chainDirofilaria_immitis.sql 2019-01-13 03:57 1.8K chainDirofilaria_immitis.txt.gz 2019-01-13 03:57 1.6M chainDirofilaria_immitisLink.sql 2019-01-13 03:57 1.6K chainDirofilaria_immitisLink.txt.gz 2019-01-13 03:57 13M chainDitylenchus_destructor.sql 2019-01-13 03:57 1.8K chainDitylenchus_destructor.txt.gz 2019-01-13 03:57 1.4M chainDitylenchus_destructorLink.sql 2019-01-13 03:57 1.6K chainDitylenchus_destructorLink.txt.gz 2019-01-13 03:57 8.4M chainDugesia_japonica.sql 2019-01-13 03:57 1.7K chainDugesia_japonica.txt.gz 2019-01-13 03:57 2.2M chainDugesia_japonicaLink.sql 2019-01-13 03:57 1.6K chainDugesia_japonicaLink.txt.gz 2019-01-13 03:57 15M chainEchinococcus_canadensis.sql 2019-01-13 03:57 1.8K chainEchinococcus_canadensis.txt.gz 2019-01-13 03:57 442K chainEchinococcus_canadensisLink.sql 2019-01-13 03:57 1.6K chainEchinococcus_canadensisLink.txt.gz 2019-01-13 03:57 1.8M chainEchinococcus_granulosus.sql 2019-01-13 03:57 1.8K chainEchinococcus_granulosus.txt.gz 2019-01-13 03:57 392K chainEchinococcus_granulosusLink.sql 2019-01-13 03:57 1.6K chainEchinococcus_granulosusLink.txt.gz 2019-01-13 03:57 1.7M chainEchinococcus_multilocularis.sql 2019-01-13 03:57 1.8K chainEchinococcus_multilocularis.txt.gz 2019-01-13 03:57 439K chainEchinococcus_multilocularisLink.sql 2019-01-13 03:57 1.6K chainEchinococcus_multilocularisLink.txt.gz 2019-01-13 03:57 1.9M chainElaeophora_elaphi.sql 2019-01-13 03:57 1.7K chainElaeophora_elaphi.txt.gz 2019-01-13 03:57 9.9K chainElaeophora_elaphiLink.sql 2019-01-13 03:57 1.6K chainElaeophora_elaphiLink.txt.gz 2019-01-13 03:57 41K chainFasciola_gigantica.sql 2019-01-13 03:57 1.7K chainFasciola_gigantica.txt.gz 2019-01-13 03:57 761K chainFasciola_giganticaLink.sql 2019-01-13 03:57 1.6K chainFasciola_giganticaLink.txt.gz 2019-01-13 03:57 2.1M chainFasciola_hepatica.sql 2019-01-13 03:57 1.7K chainFasciola_hepatica.txt.gz 2019-01-13 03:57 850K chainFasciola_hepaticaLink.sql 2019-01-13 03:57 1.6K chainFasciola_hepaticaLink.txt.gz 2019-01-13 03:57 2.6M chainGirardia_tigrina.sql 2019-01-13 03:57 1.7K chainGirardia_tigrina.txt.gz 2019-01-13 03:57 4.9M chainGirardia_tigrinaLink.sql 2019-01-13 03:57 1.6K chainGirardia_tigrinaLink.txt.gz 2019-01-13 03:58 50M chainGlobodera_ellingtonae.sql 2019-01-13 03:58 1.8K chainGlobodera_ellingtonae.txt.gz 2019-01-13 03:58 1.2M chainGlobodera_ellingtonaeLink.sql 2019-01-13 03:58 1.6K chainGlobodera_ellingtonaeLink.txt.gz 2019-01-13 03:58 7.2M chainGlobodera_pallida.sql 2019-01-13 03:58 1.7K chainGlobodera_pallida.txt.gz 2019-01-13 03:58 1.2M chainGlobodera_pallidaLink.sql 2019-01-13 03:58 1.6K chainGlobodera_pallidaLink.txt.gz 2019-01-13 03:58 6.7M chainGlobodera_rostochiensis.sql 2019-01-13 03:58 1.8K chainGlobodera_rostochiensis.txt.gz 2019-01-13 03:58 1.2M chainGlobodera_rostochiensisLink.sql 2019-01-13 03:58 1.6K chainGlobodera_rostochiensisLink.txt.gz 2019-01-13 03:58 6.6M chainGyrodactylus_salaris.sql 2019-01-13 03:58 1.8K chainGyrodactylus_salaris.txt.gz 2019-01-13 03:58 480K chainGyrodactylus_salarisLink.sql 2019-01-13 03:58 1.6K chainGyrodactylus_salarisLink.txt.gz 2019-01-13 03:58 3.3M chainHaeCon2.sql 2019-01-13 03:58 1.7K chainHaeCon2.txt.gz 2019-01-13 03:58 1.0M chainHaeCon2Link.sql 2019-01-13 03:58 1.5K chainHaeCon2Link.txt.gz 2019-01-13 03:58 3.7M chainHaemonchus_contortus.sql 2019-01-13 03:58 1.8K chainHaemonchus_contortus.txt.gz 2019-01-13 03:58 5.5M chainHaemonchus_contortusLink.sql 2019-01-13 03:58 1.6K chainHaemonchus_contortusLink.txt.gz 2019-01-13 03:58 17M chainHeligmosomoides_polygyrus_bakeri.sql 2019-01-13 03:58 1.8K chainHeligmosomoides_polygyrus_bakeri.txt.gz 2019-01-13 03:58 4.5M chainHeligmosomoides_polygyrus_bakeriLink.sql 2019-01-13 03:58 1.6K chainHeligmosomoides_polygyrus_bakeriLink.txt.gz 2019-01-13 03:58 14M chainHetBac1.sql 2019-01-13 03:58 1.7K chainHetBac1.txt.gz 2019-01-13 03:58 681K chainHetBac1Link.sql 2019-01-13 03:58 1.5K chainHetBac1Link.txt.gz 2019-01-13 03:58 3.3M chainHeterodera_glycines.sql 2019-01-13 03:58 1.8K chainHeterodera_glycines.txt.gz 2019-01-13 03:58 888K chainHeterodera_glycinesLink.sql 2019-01-13 03:58 1.6K chainHeterodera_glycinesLink.txt.gz 2019-01-13 03:58 3.9M chainHymenolepis_microstoma.sql 2019-01-13 03:58 1.8K chainHymenolepis_microstoma.txt.gz 2019-01-13 03:58 560K chainHymenolepis_microstomaLink.sql 2019-01-13 03:58 1.6K chainHymenolepis_microstomaLink.txt.gz 2019-01-13 03:58 3.1M chainLoaLoa1.sql 2019-01-13 03:58 1.7K chainLoaLoa1.txt.gz 2019-01-13 03:58 380K chainLoaLoa1Link.sql 2019-01-13 03:58 1.5K chainLoaLoa1Link.txt.gz 2019-01-13 03:58 1.4M chainLoa_loa.sql 2019-01-13 03:58 1.7K chainLoa_loa.txt.gz 2019-01-13 03:58 1.5M chainLoa_loaLink.sql 2019-01-13 03:58 1.5K chainLoa_loaLink.txt.gz 2019-01-13 03:58 10M chainMacrostomum_lignano.sql 2019-01-13 03:58 1.8K chainMacrostomum_lignano.txt.gz 2019-01-13 03:58 13M chainMacrostomum_lignanoLink.sql 2019-01-13 03:58 1.6K chainMacrostomum_lignanoLink.txt.gz 2019-01-13 03:58 38M chainMelHap1.sql 2019-01-13 03:58 1.7K chainMelHap1.txt.gz 2019-01-13 03:58 268K chainMelHap1Link.sql 2019-01-13 03:58 1.5K chainMelHap1Link.txt.gz 2019-01-13 03:58 1.2M chainMelInc2.sql 2019-01-13 03:58 1.7K chainMelInc2.txt.gz 2019-01-13 03:58 361K chainMelInc2Link.sql 2019-01-13 03:58 1.5K chainMelInc2Link.txt.gz 2019-01-13 03:58 1.5M chainMeloidogyne_arenaria.sql 2019-01-13 03:58 1.8K chainMeloidogyne_arenaria.txt.gz 2019-01-13 03:58 4.0M chainMeloidogyne_arenariaLink.sql 2019-01-13 03:58 1.6K chainMeloidogyne_arenariaLink.txt.gz 2019-01-13 03:58 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