This directory contains a dump of the UCSC genome annotation database for the
    Jul. 2013 (C_griseus_v1.0/criGri1) assembly of the chinese hamster genome
    (criGri1, Beijing Genomics Institution-Shenzhen) .

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/2791
    http://www.ncbi.nlm.nih.gov/genome/assembly/40911
    http://www.ncbi.nlm.nih.gov/bioproject/167053

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=criGri1
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/criGri1/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/criGri1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/criGri1/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 criGri1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql criGri1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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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 2020-08-18 20:53 44M xenoRefSeqAli.sql 2020-08-18 20:53 2.1K xenoRefGene.txt.gz 2020-08-18 20:40 42M xenoRefGene.sql 2020-08-18 20:40 2.0K xenoRefFlat.txt.gz 2020-08-18 20:53 38M xenoRefFlat.sql 2020-08-18 20:53 1.7K xenoMrna.txt.gz 2018-07-29 05:38 33 xenoMrna.sql 2018-07-29 05:38 2.1K windowmaskerSdust.txt.gz 2014-05-08 12:04 84M windowmaskerSdust.sql 2014-05-08 12:03 1.5K ucscToINSDC.txt.gz 2014-05-08 12:03 307K ucscToINSDC.sql 2014-05-08 12:03 1.4K trackDb.txt.gz 2023-03-28 13:47 39K trackDb.sql 2023-03-28 13:47 2.1K tableList.txt.gz 2024-12-08 03:29 2.7K tableList.sql 2024-12-08 03:29 1.6K tableDescriptions.txt.gz 2024-12-07 02:03 5.3K tableDescriptions.sql 2024-12-07 02:03 1.4K simpleRepeat.txt.gz 2014-05-08 12:03 23M simpleRepeat.sql 2014-05-08 12:03 1.9K rmsk.txt.gz 2014-05-08 12:03 101M rmsk.sql 2014-05-08 12:03 1.9K refSeqAli.txt.gz 2020-05-06 06:20 44K refSeqAli.sql 2020-05-06 06:20 2.1K refGene.txt.gz 2020-08-18 20:36 39K refGene.sql 2020-08-18 20:36 1.9K refFlat.txt.gz 2020-08-18 20:36 36K refFlat.sql 2020-08-18 20:36 1.7K netHg19.txt.gz 2014-05-08 12:02 51M netHg19.sql 2014-05-08 12:02 2.1K netCriGriChoV1.txt.gz 2017-11-26 06:38 16M netCriGriChoV1.sql 2017-11-26 06:38 2.1K nestedRepeats.txt.gz 2014-05-08 11:57 8.9M nestedRepeats.sql 2014-05-08 11:57 1.9K mrnaOrientInfo.txt.gz 2020-05-06 06:16 802K mrnaOrientInfo.sql 2020-05-06 06:16 1.8K microsat.txt.gz 2015-08-23 12:50 2.0M microsat.sql 2015-08-23 12:50 1.5K locusName.txt.gz 2017-08-20 09:02 9.1M locusName.sql 2017-08-20 09:02 1.5K intronEst.txt.gz 2014-05-08 11:56 533 intronEst.sql 2014-05-08 11:56 2.1K history.txt.gz 2014-05-08 12:03 466 history.sql 2014-05-08 12:03 1.6K hgFindSpec.txt.gz 2023-03-28 13:47 697 hgFindSpec.sql 2023-03-28 13:47 1.8K grp.txt.gz 2014-05-08 12:03 206 grp.sql 2014-05-08 12:03 1.3K gold.txt.gz 2014-05-08 12:03 3.0M gold.sql 2014-05-08 12:03 1.7K genscan.txt.gz 2014-05-08 12:03 3.0M genscan.sql 2014-05-08 12:03 1.7K gc5BaseBw.txt.gz 2014-05-08 12:03 66 gc5BaseBw.sql 2014-05-08 12:03 1.3K gbLoaded.txt.gz 2020-08-18 20:53 65K gbLoaded.sql 2020-08-18 20:53 1.6K gap.txt.gz 2014-05-08 12:03 2.0M gap.sql 2014-05-08 12:03 1.6K estOrientInfo.txt.gz 2014-05-08 12:03 278 estOrientInfo.sql 2014-05-08 12:03 1.8K cytoBandIdeo.txt.gz 2014-05-08 12:03 185K cytoBandIdeo.sql 2014-05-08 12:03 1.5K crisprTargets.txt.gz 2017-08-20 09:02 61 crisprTargets.sql 2017-08-20 09:02 1.3K crisprRanges.txt.gz 2017-08-20 09:02 2.1M crisprRanges.sql 2017-08-20 09:02 1.4K cpgIslandExtUnmasked.txt.gz 2014-05-08 12:03 309K cpgIslandExtUnmasked.sql 2014-05-08 12:03 1.7K cpgIslandExt.txt.gz 2014-05-08 12:03 290K cpgIslandExt.sql 2014-05-08 12:03 1.7K chromInfo.txt.gz 2014-05-08 12:02 200K chromInfo.sql 2014-05-08 12:02 1.4K chainHg19Link.txt.gz 2014-05-08 11:59 1.0G chainHg19Link.sql 2014-05-08 11:57 1.5K chainHg19.txt.gz 2014-05-08 11:56 266M chainHg19.sql 2014-05-08 11:56 1.7K chainCriGriChoV1Link.txt.gz 2017-11-26 06:25 3.5G chainCriGriChoV1Link.sql 2017-11-26 06:20 1.6K chainCriGriChoV1.txt.gz 2017-11-26 06:18 788M chainCriGriChoV1.sql 2017-11-26 06:17 1.7K bigFiles.txt.gz 2024-12-08 03:29 92 bigFiles.sql 2024-12-08 03:29 1.4K augustusGene.txt.gz 2015-07-26 11:46 2.1M augustusGene.sql 2015-07-26 11:46 1.9K all_mrna.txt.gz 2018-11-04 06:14 2.9M all_mrna.sql 2018-11-04 06:14 2.1K all_est.txt.gz 2014-05-08 11:56 790 all_est.sql 2014-05-08 11:56 2.1K