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 - gbWarn.txt.gz 2017-07-21 10:14 31 imageClone.txt.gz 2017-07-21 10:14 35 sex.txt.gz 2017-07-21 10:14 39 cell.txt.gz 2017-07-21 10:13 40 gc5BaseBw.txt.gz 2017-07-21 10:14 62 bigFiles.txt.gz 2022-08-14 03:04 65 grp.txt.gz 2017-07-21 10:14 213 development.txt.gz 2017-07-21 10:13 442 tissue.txt.gz 2017-07-21 10:14 617 hgFindSpec.txt.gz 2021-12-27 12:23 775 history.txt.gz 2017-07-21 10:14 785 library.txt.gz 2017-07-21 10:14 914 gc5BaseBw.sql 2017-07-21 10:14 1.3K gbWarn.sql 2017-07-21 10:14 1.3K ensPep.sql 2021-05-25 14:25 1.3K grp.sql 2017-07-21 10:14 1.3K bigFiles.sql 2022-08-14 03:04 1.4K ensemblSource.sql 2021-05-25 14:25 1.4K chromInfo.sql 2017-07-21 10:13 1.4K cds.sql 2017-07-21 10:13 1.4K sex.sql 2017-07-21 10:14 1.4K cell.sql 2017-07-21 10:13 1.4K author.sql 2017-07-21 10:13 1.4K source.sql 2017-07-21 10:14 1.4K tissue.sql 2017-07-21 10:14 1.4K gbExtFile.sql 2017-07-21 10:13 1.4K keyword.sql 2017-07-21 10:14 1.4K library.sql 2017-07-21 10:14 1.4K geneName.sql 2017-07-21 10:14 1.4K organism.sql 2017-07-21 10:14 1.4K ensemblToGeneName.sql 2021-05-25 14:25 1.4K mrnaClone.sql 2017-07-21 10:14 1.4K tableDescriptions.sql 2019-07-21 03:41 1.4K description.sql 2017-07-21 10:13 1.4K development.sql 2017-07-21 10:13 1.4K productName.sql 2017-07-21 10:14 1.4K chromAlias.sql 2017-07-21 10:13 1.4K ucscToINSDC.sql 2017-07-21 10:14 1.4K ucscToRefSeq.sql 2017-07-21 10:14 1.4K ensGtp.sql 2021-05-25 14:25 1.4K gbMiscDiff.sql 2017-07-21 10:13 1.5K gbMiscDiff.txt.gz 2017-07-21 10:13 1.5K microsat.sql 2017-07-21 10:14 1.5K refSeqSummary.sql 2017-07-21 10:14 1.5K imageClone.sql 2017-07-21 10:14 1.5K windowmaskerSdust.sql 2017-07-21 10:14 1.5K cytoBandIdeo.sql 2017-07-21 10:13 1.5K chainCe11Link.sql 2017-07-21 10:13 1.5K chainStrPur2Link.sql 2017-07-21 10:13 1.5K tableList.sql 2022-08-14 03:04 1.6K history.sql 2017-07-21 10:14 1.6K gbLoaded.sql 2017-07-21 10:13 1.6K gap.sql 2017-07-21 10:13 1.6K refSeqStatus.sql 2017-07-21 10:14 1.6K gold.sql 2017-07-21 10:14 1.7K genscan.sql 2017-07-21 10:14 1.7K cpgIslandExt.sql 2017-07-21 10:13 1.7K chainCe11.sql 2017-07-21 10:13 1.7K gbSeq.sql 2017-07-21 10:13 1.7K refFlat.sql 2017-07-21 10:14 1.7K chainStrPur2.sql 2017-07-21 10:13 1.7K cpgIslandExtUnmasked.sql 2017-07-21 10:13 1.7K xenoRefFlat.sql 2017-07-21 10:14 1.7K refLink.sql 2017-07-21 10:14 1.7K hgFindSpec.sql 2021-12-27 12:23 1.8K microsat.txt.gz 2017-07-21 10:14 1.8K estOrientInfo.sql 2017-07-21 10:13 1.8K mrnaOrientInfo.sql 2017-07-21 10:14 1.8K rmsk.sql 2017-07-21 10:14 1.9K gbStatus.sql 2017-07-21 10:13 1.9K refGene.sql 2017-07-21 10:14 1.9K simpleRepeat.sql 2017-07-21 10:14 1.9K nestedRepeats.sql 2017-07-21 10:14 1.9K xenoRefGene.sql 2017-07-21 10:14 1.9K ensGene.sql 2021-05-25 14:25 1.9K trackDb.sql 2021-12-27 12:23 2.1K netCe11.sql 2017-07-21 10:14 2.1K netStrPur2.sql 2017-07-21 10:14 2.1K all_est.sql 2017-07-21 10:13 2.1K all_mrna.sql 2017-07-21 10:13 2.1K intronEst.sql 2017-07-21 10:14 2.1K refSeqAli.sql 2017-07-21 10:14 2.1K xenoRefSeqAli.sql 2017-07-21 10:14 2.1K gbCdnaInfo.sql 2017-07-21 10:13 2.6K tableList.txt.gz 2022-08-14 03:04 3.6K keyword.txt.gz 2017-07-21 10:14 3.6K ensemblToGeneName.txt.gz 2021-05-25 14:25 5.8K tableDescriptions.txt.gz 2019-07-21 03:41 7.2K cytoBandIdeo.txt.gz 2017-07-21 10:13 7.6K chromInfo.txt.gz 2017-07-21 10:13 7.8K gbExtFile.txt.gz 2017-07-21 10:13 10K ucscToRefSeq.txt.gz 2017-07-21 10:14 11K ucscToINSDC.txt.gz 2017-07-21 10:14 11K chromAlias.txt.gz 2017-07-21 10:13 13K gbLoaded.txt.gz 2017-07-21 10:13 15K trackDb.txt.gz 2021-12-27 12:23 27K cpgIslandExt.txt.gz 2017-07-21 10:13 28K cpgIslandExtUnmasked.txt.gz 2017-07-21 10:13 36K ensemblSource.txt.gz 2021-05-25 14:25 51K gap.txt.gz 2017-07-21 10:13 59K refFlat.txt.gz 2017-07-21 10:14 87K refGene.txt.gz 2017-07-21 10:14 96K gold.txt.gz 2017-07-21 10:14 100K refSeqAli.txt.gz 2017-07-21 10:14 102K mrnaOrientInfo.txt.gz 2017-07-21 10:14 149K ensGtp.txt.gz 2021-05-25 14:25 184K nestedRepeats.txt.gz 2017-07-21 10:14 205K netCe11.txt.gz 2017-07-21 10:14 304K organism.txt.gz 2017-07-21 10:14 306K source.txt.gz 2017-07-21 10:14 313K chainCe11.txt.gz 2017-07-21 10:13 315K genscan.txt.gz 2017-07-21 10:14 415K all_mrna.txt.gz 2017-07-21 10:13 676K chainCe11Link.txt.gz 2017-07-21 10:13 706K netStrPur2.txt.gz 2017-07-21 10:14 791K simpleRepeat.txt.gz 2017-07-21 10:14 1.1M ensGene.txt.gz 2021-05-25 14:25 1.2M refSeqStatus.txt.gz 2017-07-21 10:14 1.5M chainStrPur2.txt.gz 2017-07-21 10:13 1.5M cds.txt.gz 2017-07-21 10:13 2.1M rmsk.txt.gz 2017-07-21 10:14 3.2M ensPep.txt.gz 2021-05-25 14:25 3.3M chainStrPur2Link.txt.gz 2017-07-21 10:13 3.5M productName.txt.gz 2017-07-21 10:14 3.6M xenoRefSeqAli.txt.gz 2017-07-21 10:14 3.9M author.txt.gz 2017-07-21 10:13 4.1M geneName.txt.gz 2017-07-21 10:14 4.2M xenoRefFlat.txt.gz 2017-07-21 10:14 4.2M xenoRefGene.txt.gz 2017-07-21 10:14 4.7M refSeqSummary.txt.gz 2017-07-21 10:14 5.2M mrnaClone.txt.gz 2017-07-21 10:14 5.7M windowmaskerSdust.txt.gz 2017-07-21 10:14 7.5M refLink.txt.gz 2017-07-21 10:14 11M estOrientInfo.txt.gz 2017-07-21 10:13 11M gbStatus.txt.gz 2017-07-21 10:13 11M description.txt.gz 2017-07-21 10:13 13M gbCdnaInfo.txt.gz 2017-07-21 10:13 22M intronEst.txt.gz 2017-07-21 10:14 26M gbSeq.txt.gz 2017-07-21 10:13 29M all_est.txt.gz 2017-07-21 10:13 39M