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 - bigFiles.txt.gz 2024-11-24 03:26 113 bigFiles.sql 2024-11-24 03:26 1.4K tableList.txt.gz 2024-11-24 03:26 16K tableList.sql 2024-11-24 03:26 1.6K tableDescriptions.txt.gz 2024-11-23 02:03 13K tableDescriptions.sql 2024-11-23 02:03 1.4K hgFindSpec.txt.gz 2023-12-05 13:52 1.2K hgFindSpec.sql 2023-12-05 13:52 1.8K trackDb.txt.gz 2023-12-05 13:52 72K trackDb.sql 2023-12-05 13:52 2.1K mmBlastTab.txt.gz 2022-07-12 17:09 122K mmBlastTab.sql 2022-07-12 17:09 1.7K hgBlastTab.txt.gz 2022-07-12 17:02 117K hgBlastTab.sql 2022-07-12 17:02 1.7K ensPep.txt.gz 2021-05-25 14:25 5.0M ensPep.sql 2021-05-25 14:25 1.3K ensemblSource.txt.gz 2021-05-25 14:25 186K ensemblSource.sql 2021-05-25 14:25 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:23 312K ensemblToGeneName.sql 2021-05-25 14:23 1.4K 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 gbLoaded.txt.gz 2020-08-18 14:30 46K gbLoaded.sql 2020-08-18 14:30 1.6K xenoRefSeqAli.txt.gz 2020-08-18 14:25 1.5M xenoRefSeqAli.sql 2020-08-18 14:25 2.1K refSeqAli.txt.gz 2020-08-18 14:25 2.6M refSeqAli.sql 2020-08-18 14:25 2.1K mrnaOrientInfo.txt.gz 2020-08-18 14:25 825K mrnaOrientInfo.sql 2020-08-18 14:25 1.8K xenoRefFlat.txt.gz 2020-08-18 14:25 1.5M xenoRefFlat.sql 2020-08-18 14:25 1.7K xenoRefGene.txt.gz 2020-08-18 14:25 1.7M xenoRefGene.sql 2020-08-18 14:25 2.0K refFlat.txt.gz 2020-08-18 14:25 2.1M refFlat.sql 2020-08-18 14:25 1.7K refGene.txt.gz 2020-08-18 14:25 2.3M refGene.sql 2020-08-18 14:25 1.9K xenoMrna.txt.gz 2020-08-18 14:04 33M xenoMrna.sql 2020-08-18 14:04 2.1K all_mrna.txt.gz 2020-08-18 14:04 317K all_mrna.sql 2020-08-18 14:04 2.1K seqNcbiRefSeq.txt.gz 2020-07-02 16:49 674K seqNcbiRefSeq.sql 2020-07-02 16:49 1.6K extNcbiRefSeq.txt.gz 2020-07-02 16:38 87 extNcbiRefSeq.sql 2020-07-02 16:38 1.5K ncbiRefSeqPepTable.txt.gz 2020-07-02 16:38 6.1M ncbiRefSeqPepTable.sql 2020-07-02 16:38 1.4K ncbiRefSeqCds.txt.gz 2020-07-02 16:38 183K ncbiRefSeqCds.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 ncbiRefSeqPsl.txt.gz 2020-07-02 15:50 2.4M ncbiRefSeqPsl.sql 2020-07-02 15:50 2.1K 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 ncbiRefSeq.txt.gz 2020-07-02 15:50 2.2M ncbiRefSeq.sql 2020-07-02 15:50 1.9K phyloP135way.txt.gz 2019-01-13 04:04 3.0M phyloP135way.sql 2019-01-13 04:04 1.8K phastConsElements135way.txt.gz 2019-01-13 04:04 19M phastConsElements135way.sql 2019-01-13 04:04 1.6K phastCons135way.txt.gz 2019-01-13 04:04 2.5M phastCons135way.sql 2019-01-13 04:04 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 netCaeSp51.txt.gz 2019-01-13 04:04 3.4M netCaeSp51.sql 2019-01-13 04:04 2.1K netCaeSp111.txt.gz 2019-01-13 04:04 4.1M netCaeSp111.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 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 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 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 04:02 40M chainStrongyloides_papillosusLink.sql 2019-01-13 04:02 1.6K chainStrongyloides_papillosus.txt.gz 2019-01-13 04:02 4.8M chainStrongyloides_papillosus.sql 2019-01-13 04:02 1.8K chainStrRat2Link.txt.gz 2019-01-13 04:02 53M chainStrRat2Link.sql 2019-01-13 04:01 1.5K chainStrRat2.txt.gz 2019-01-13 04:01 4.0M chainStrRat2.sql 2019-01-13 04:01 1.7K chainSteinernema_scapterisciLink.txt.gz 2019-01-13 04:01 9.2M chainSteinernema_scapterisciLink.sql 2019-01-13 04:01 1.6K chainSteinernema_scapterisci.txt.gz 2019-01-13 04:01 2.1M chainSteinernema_scapterisci.sql 2019-01-13 04:01 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chainSpirometra_erinaceieuropaeiLink.sql 2019-01-13 04:01 1.6K chainSpirometra_erinaceieuropaei.txt.gz 2019-01-13 04:01 896K chainSpirometra_erinaceieuropaei.sql 2019-01-13 04:01 1.8K chainSetaria_equinaLink.txt.gz 2019-01-13 04:01 8.3M chainSetaria_equinaLink.sql 2019-01-13 04:01 1.6K chainSetaria_equina.txt.gz 2019-01-13 04:01 1.4M chainSetaria_equina.sql 2019-01-13 04:01 1.7K chainSetaria_digitataLink.txt.gz 2019-01-13 04:01 8.5M chainSetaria_digitataLink.sql 2019-01-13 04:01 1.6K chainSetaria_digitata.txt.gz 2019-01-13 04:01 1.1M chainSetaria_digitata.sql 2019-01-13 04:01 1.7K chainSchmidtea_mediterraneaLink.txt.gz 2019-01-13 04:01 62M chainSchmidtea_mediterraneaLink.sql 2019-01-13 04:01 1.6K chainSchmidtea_mediterranea.txt.gz 2019-01-13 04:01 4.6M chainSchmidtea_mediterranea.sql 2019-01-13 04:01 1.8K chainSchistosoma_mansoniLink.txt.gz 2019-01-13 04:01 5.8M chainSchistosoma_mansoniLink.sql 2019-01-13 04:01 1.6K chainSchistosoma_mansoni.txt.gz 2019-01-13 04:01 1.0M 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