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