This directory contains a dump of the UCSC genome annotation database for
the Jul. 2008 (Broad/ochPri2) assembly of the pika genome (ochPri2, Broad Institute ochPri2).
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/771
    http://www.ncbi.nlm.nih.gov/genome/assembly/199698
    http://www.ncbi.nlm.nih.gov/bioproject/19235

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=ochPri2
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

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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/ochPri2/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/ochPri2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/ochPri2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri2/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri2/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 ochPri2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ochPri2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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The Pika sequence is made freely available before scientific publication 
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 particular 
      genes and regions if the provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves 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. 1. The data may 
      be freely downloaded, used in analyses, and repackaged in databases.

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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.

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All the files and tables in this directory are freely usable for any purpose.
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      Name                        Last modified      Size  Description
Parent Directory - genscan.sql 2012-11-21 15:49 1.7K genscan.txt.gz 2012-11-21 15:49 4.6M history.sql 2012-11-21 15:49 1.6K history.txt.gz 2012-11-21 15:49 955 rmsk.sql 2012-11-21 15:49 2.1K rmsk.txt.gz 2012-11-21 15:49 37M simpleRepeat.sql 2012-11-21 15:49 2.1K simpleRepeat.txt.gz 2012-11-21 15:49 16M gap.sql 2012-11-21 15:50 1.7K gap.txt.gz 2012-11-21 15:50 6.2M gc5Base.sql 2012-11-21 15:50 1.9K gc5Base.txt.gz 2012-11-21 15:50 15M cpgIslandExt.sql 2012-11-21 15:50 1.7K cpgIslandExt.txt.gz 2012-11-21 15:50 1.0M nestedRepeats.sql 2012-11-21 15:50 2.1K nestedRepeats.txt.gz 2012-11-21 15:50 2.7M windowmaskerSdust.sql 2012-11-21 15:50 1.5K windowmaskerSdust.txt.gz 2012-11-21 15:50 90M chromInfo.sql 2012-11-21 15:50 1.4K chromInfo.txt.gz 2012-11-21 15:50 773K netMm10.sql 2012-11-21 15:50 2.1K netMm10.txt.gz 2012-11-21 15:50 30M quality.sql 2012-11-21 15:50 1.9K quality.txt.gz 2012-11-21 15:51 65M chainMm10Link.sql 2012-11-21 15:51 1.5K chainMm10Link.txt.gz 2012-11-21 15:51 253M chainMm10.sql 2012-11-21 15:52 1.7K chainMm10.txt.gz 2012-11-21 15:52 45M gold.sql 2012-11-21 15:53 1.8K gold.txt.gz 2012-11-21 15:53 9.3M cytoBandIdeo.sql 2013-04-28 19:27 1.5K cytoBandIdeo.txt.gz 2013-04-28 19:27 765K grp.sql 2014-03-02 04:14 1.4K grp.txt.gz 2014-03-02 04:14 208 cpgIslandExtUnmasked.sql 2014-06-01 17:29 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 17:29 1.0M augustusGene.sql 2015-07-26 17:03 1.9K augustusGene.txt.gz 2015-07-26 17:03 2.1M microsat.sql 2015-08-23 22:30 1.5K microsat.txt.gz 2015-08-23 22:30 297K chromAlias.sql 2018-08-05 08:27 1.4K chromAlias.txt.gz 2018-08-05 08:27 1.8M ensGtp.sql 2019-02-10 03:42 1.4K ensGtp.txt.gz 2019-02-10 03:42 230K ensPep.sql 2019-02-10 03:42 1.3K ensPep.txt.gz 2019-02-10 03:42 4.6M ensemblGeneScaffold.sql 2019-02-10 03:42 1.7K ensemblGeneScaffold.txt.gz 2019-02-10 03:42 576K ensemblSource.sql 2019-02-10 03:42 1.4K ensemblSource.txt.gz 2019-02-10 03:42 70K ensemblToGeneName.sql 2019-02-10 03:42 1.4K ensemblToGeneName.txt.gz 2019-02-10 03:42 104K ensGene.sql 2019-02-10 03:42 1.9K ensGene.txt.gz 2019-02-10 03:42 2.0M mrnaOrientInfo.sql 2019-03-17 11:36 1.8K mrnaOrientInfo.txt.gz 2019-03-17 11:36 185 all_mrna.sql 2019-03-17 11:37 2.1K all_mrna.txt.gz 2019-03-17 11:37 436 tableDescriptions.sql 2019-07-21 03:43 1.4K tableDescriptions.txt.gz 2019-07-21 03:43 5.5K xenoRefGene.sql 2020-08-22 14:19 1.9K xenoRefGene.txt.gz 2020-08-22 14:19 37M gbLoaded.sql 2020-08-22 14:19 1.6K xenoRefFlat.sql 2020-08-22 14:19 1.7K xenoRefSeqAli.sql 2020-08-22 14:19 2.1K xenoRefFlat.txt.gz 2020-08-22 14:19 33M xenoRefSeqAli.txt.gz 2020-08-22 14:19 40M gbLoaded.txt.gz 2020-08-22 14:19 30K trackDb.sql 2021-06-10 16:54 2.1K trackDb.txt.gz 2021-06-10 16:54 20K hgFindSpec.sql 2021-06-10 16:54 1.8K hgFindSpec.txt.gz 2021-06-10 16:54 698 tableList.sql 2021-06-20 03:05 1.6K tableList.txt.gz 2021-06-20 03:05 2.3K bigFiles.sql 2021-06-20 03:05 1.4K bigFiles.txt.gz 2021-06-20 03:05 33