This directory contains a dump of the UCSC genome annotation database for the
    Apr. 2011 (Kyoto KH/ci3) assembly of the C. intestinalis genome
    (ci3, Kyoto KH) .

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/49
    http://www.ncbi.nlm.nih.gov/genome/assembly/527578
    http://www.ncbi.nlm.nih.gov/bioproject/187185

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=ci3
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/ci3/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/ci3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ci3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ci3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ci3/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 ci3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ci3 --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 - all_est.sql 2017-07-21 10:13 2.1K all_est.txt.gz 2017-07-21 10:13 39M all_mrna.sql 2017-07-21 10:13 2.1K all_mrna.txt.gz 2017-07-21 10:13 676K author.sql 2017-07-21 10:13 1.4K author.txt.gz 2017-07-21 10:13 4.1M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 65 cds.sql 2017-07-21 10:13 1.4K cds.txt.gz 2017-07-21 10:13 2.1M cell.sql 2017-07-21 10:13 1.4K cell.txt.gz 2017-07-21 10:13 40 chainCe11.sql 2017-07-21 10:13 1.7K chainCe11.txt.gz 2017-07-21 10:13 315K chainCe11Link.sql 2017-07-21 10:13 1.5K chainCe11Link.txt.gz 2017-07-21 10:13 706K chainStrPur2.sql 2017-07-21 10:13 1.7K chainStrPur2.txt.gz 2017-07-21 10:13 1.5M chainStrPur2Link.sql 2017-07-21 10:13 1.5K chainStrPur2Link.txt.gz 2017-07-21 10:13 3.5M chromAlias.sql 2017-07-21 10:13 1.4K chromAlias.txt.gz 2017-07-21 10:13 13K chromInfo.sql 2017-07-21 10:13 1.4K chromInfo.txt.gz 2017-07-21 10:13 7.8K cpgIslandExt.sql 2017-07-21 10:13 1.7K cpgIslandExt.txt.gz 2017-07-21 10:13 28K cpgIslandExtUnmasked.sql 2017-07-21 10:13 1.7K cpgIslandExtUnmasked.txt.gz 2017-07-21 10:13 36K cytoBandIdeo.sql 2017-07-21 10:13 1.5K cytoBandIdeo.txt.gz 2017-07-21 10:13 7.6K description.sql 2017-07-21 10:13 1.4K description.txt.gz 2017-07-21 10:13 13M development.sql 2017-07-21 10:13 1.4K development.txt.gz 2017-07-21 10:13 442 ensGene.sql 2020-08-31 15:25 1.9K ensGene.txt.gz 2020-08-31 15:25 1.2M ensGtp.sql 2020-08-31 15:25 1.4K ensGtp.txt.gz 2020-08-31 15:25 184K ensPep.sql 2020-08-31 15:49 1.3K ensPep.txt.gz 2020-08-31 15:49 3.3M ensemblSource.sql 2020-08-31 15:48 1.3K ensemblSource.txt.gz 2020-08-31 15:48 51K ensemblToGeneName.sql 2020-08-31 15:25 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:25 5.8K estOrientInfo.sql 2017-07-21 10:13 1.8K estOrientInfo.txt.gz 2017-07-21 10:13 11M gap.sql 2017-07-21 10:13 1.6K gap.txt.gz 2017-07-21 10:13 59K gbCdnaInfo.sql 2017-07-21 10:13 2.6K gbCdnaInfo.txt.gz 2017-07-21 10:13 22M gbExtFile.sql 2017-07-21 10:13 1.4K gbExtFile.txt.gz 2017-07-21 10:13 10K gbLoaded.sql 2017-07-21 10:13 1.6K gbLoaded.txt.gz 2017-07-21 10:13 15K gbMiscDiff.sql 2017-07-21 10:13 1.5K gbMiscDiff.txt.gz 2017-07-21 10:13 1.5K gbSeq.sql 2017-07-21 10:13 1.7K gbSeq.txt.gz 2017-07-21 10:13 29M gbStatus.sql 2017-07-21 10:13 1.9K gbStatus.txt.gz 2017-07-21 10:13 11M gbWarn.sql 2017-07-21 10:14 1.3K gbWarn.txt.gz 2017-07-21 10:14 31 gc5BaseBw.sql 2017-07-21 10:14 1.3K gc5BaseBw.txt.gz 2017-07-21 10:14 62 geneName.sql 2017-07-21 10:14 1.4K geneName.txt.gz 2017-07-21 10:14 4.2M genscan.sql 2017-07-21 10:14 1.7K genscan.txt.gz 2017-07-21 10:14 415K gold.sql 2017-07-21 10:14 1.7K gold.txt.gz 2017-07-21 10:14 100K grp.sql 2017-07-21 10:14 1.3K grp.txt.gz 2017-07-21 10:14 213 hgFindSpec.sql 2020-12-06 07:49 1.7K hgFindSpec.txt.gz 2020-12-06 07:49 775 history.sql 2017-07-21 10:14 1.6K history.txt.gz 2017-07-21 10:14 785 imageClone.sql 2017-07-21 10:14 1.5K imageClone.txt.gz 2017-07-21 10:14 35 intronEst.sql 2017-07-21 10:14 2.1K intronEst.txt.gz 2017-07-21 10:14 26M keyword.sql 2017-07-21 10:14 1.4K keyword.txt.gz 2017-07-21 10:14 3.6K library.sql 2017-07-21 10:14 1.4K library.txt.gz 2017-07-21 10:14 914 microsat.sql 2017-07-21 10:14 1.5K microsat.txt.gz 2017-07-21 10:14 1.8K mrnaClone.sql 2017-07-21 10:14 1.4K mrnaClone.txt.gz 2017-07-21 10:14 5.7M mrnaOrientInfo.sql 2017-07-21 10:14 1.8K mrnaOrientInfo.txt.gz 2017-07-21 10:14 149K nestedRepeats.sql 2017-07-21 10:14 1.9K nestedRepeats.txt.gz 2017-07-21 10:14 205K netCe11.sql 2017-07-21 10:14 2.1K netCe11.txt.gz 2017-07-21 10:14 304K netStrPur2.sql 2017-07-21 10:14 2.1K netStrPur2.txt.gz 2017-07-21 10:14 791K organism.sql 2017-07-21 10:14 1.4K organism.txt.gz 2017-07-21 10:14 306K productName.sql 2017-07-21 10:14 1.4K productName.txt.gz 2017-07-21 10:14 3.6M refFlat.sql 2017-07-21 10:14 1.7K refFlat.txt.gz 2017-07-21 10:14 87K refGene.sql 2017-07-21 10:14 1.9K refGene.txt.gz 2017-07-21 10:14 96K refLink.sql 2017-07-21 10:14 1.7K refLink.txt.gz 2017-07-21 10:14 11M refSeqAli.sql 2017-07-21 10:14 2.1K refSeqAli.txt.gz 2017-07-21 10:14 102K refSeqStatus.sql 2017-07-21 10:14 1.6K refSeqStatus.txt.gz 2017-07-21 10:14 1.5M refSeqSummary.sql 2017-07-21 10:14 1.5K refSeqSummary.txt.gz 2017-07-21 10:14 5.2M rmsk.sql 2017-07-21 10:14 1.9K rmsk.txt.gz 2017-07-21 10:14 3.2M sex.sql 2017-07-21 10:14 1.4K sex.txt.gz 2017-07-21 10:14 39 simpleRepeat.sql 2017-07-21 10:14 1.9K simpleRepeat.txt.gz 2017-07-21 10:14 1.1M source.sql 2017-07-21 10:14 1.4K source.txt.gz 2017-07-21 10:14 313K tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 7.2K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 3.6K tissue.sql 2017-07-21 10:14 1.4K tissue.txt.gz 2017-07-21 10:14 617 trackDb.sql 2020-12-06 07:49 2.0K trackDb.txt.gz 2020-12-06 07:49 25K ucscToINSDC.sql 2017-07-21 10:14 1.4K ucscToINSDC.txt.gz 2017-07-21 10:14 11K ucscToRefSeq.sql 2017-07-21 10:14 1.4K ucscToRefSeq.txt.gz 2017-07-21 10:14 11K windowmaskerSdust.sql 2017-07-21 10:14 1.5K windowmaskerSdust.txt.gz 2017-07-21 10:14 7.5M xenoRefFlat.sql 2017-07-21 10:14 1.7K xenoRefFlat.txt.gz 2017-07-21 10:14 4.2M xenoRefGene.sql 2017-07-21 10:14 1.9K xenoRefGene.txt.gz 2017-07-21 10:14 4.7M xenoRefSeqAli.sql 2017-07-21 10:14 2.1K xenoRefSeqAli.txt.gz 2017-07-21 10:14 3.9M