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 -
bigFiles.txt.gz 16-Jul-2017 06:16 33
mrnaOrientInfo.txt.gz 12-Oct-2015 06:41 163
grp.txt.gz 02-Mar-2014 04:14 208
all_mrna.txt.gz 12-Oct-2015 06:42 376
hgFindSpec.txt.gz 16-Jul-2017 06:16 628
history.txt.gz 21-Nov-2012 15:49 955
ensPep.sql 14-Sep-2015 07:03 1.3K
bigFiles.sql 16-Jul-2017 06:16 1.4K
ensemblSource.sql 14-Sep-2015 07:03 1.4K
grp.sql 02-Mar-2014 04:14 1.4K
ensemblToGeneName.sql 14-Sep-2015 07:03 1.4K
tableDescriptions.sql 16-Jul-2017 06:16 1.4K
chromInfo.sql 21-Nov-2012 15:50 1.4K
ensGtp.sql 14-Sep-2015 07:03 1.4K
microsat.sql 23-Aug-2015 22:30 1.5K
windowmaskerSdust.sql 21-Nov-2012 15:50 1.5K
cytoBandIdeo.sql 28-Apr-2013 19:27 1.5K
chainMm10Link.sql 21-Nov-2012 15:51 1.5K
tableList.sql 16-Jul-2017 06:16 1.5K
gbLoaded.sql 09-Jul-2017 11:57 1.6K
history.sql 21-Nov-2012 15:49 1.6K
ensemblGeneScaffold.sql 14-Sep-2015 07:03 1.7K
genscan.sql 21-Nov-2012 15:49 1.7K
cpgIslandExt.sql 21-Nov-2012 15:50 1.7K
gap.sql 21-Nov-2012 15:50 1.7K
chainMm10.sql 21-Nov-2012 15:52 1.7K
cpgIslandExtUnmasked.sql 01-Jun-2014 17:29 1.7K
xenoRefFlat.sql 09-Jul-2017 11:56 1.7K
hgFindSpec.sql 16-Jul-2017 06:16 1.7K
mrnaOrientInfo.sql 12-Oct-2015 06:41 1.8K
gold.sql 21-Nov-2012 15:53 1.8K
ensGene.sql 14-Sep-2015 07:02 1.9K
gc5Base.sql 21-Nov-2012 15:50 1.9K
quality.sql 21-Nov-2012 15:50 1.9K
xenoRefGene.sql 09-Jul-2017 11:56 1.9K
augustusGene.sql 26-Jul-2015 17:03 1.9K
trackDb.sql 16-Jul-2017 06:16 2.0K
rmsk.sql 21-Nov-2012 15:49 2.1K
nestedRepeats.sql 21-Nov-2012 15:50 2.1K
netMm10.sql 21-Nov-2012 15:50 2.1K
all_mrna.sql 12-Oct-2015 06:42 2.1K
simpleRepeat.sql 21-Nov-2012 15:49 2.1K
xenoRefSeqAli.sql 09-Jul-2017 11:57 2.1K
tableList.txt.gz 16-Jul-2017 06:16 2.3K
tableDescriptions.txt.gz 16-Jul-2017 06:16 4.5K
trackDb.txt.gz 16-Jul-2017 06:16 18K
gbLoaded.txt.gz 09-Jul-2017 11:57 21K
ensemblSource.txt.gz 14-Sep-2015 07:03 70K
ensemblToGeneName.txt.gz 14-Sep-2015 07:03 134K
ensGtp.txt.gz 14-Sep-2015 07:03 230K
microsat.txt.gz 23-Aug-2015 22:30 297K
cytoBandIdeo.txt.gz 28-Apr-2013 19:27 765K
chromInfo.txt.gz 21-Nov-2012 15:50 773K
cpgIslandExt.txt.gz 21-Nov-2012 15:50 1.0M
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 17:29 1.0M
ensGene.txt.gz 14-Sep-2015 07:02 2.0M
augustusGene.txt.gz 26-Jul-2015 17:03 2.1M
nestedRepeats.txt.gz 21-Nov-2012 15:50 2.7M
ensemblGeneScaffold.txt.gz 14-Sep-2015 07:03 4.3M
ensPep.txt.gz 14-Sep-2015 07:03 4.6M
genscan.txt.gz 21-Nov-2012 15:49 4.6M
gap.txt.gz 21-Nov-2012 15:50 6.2M
gold.txt.gz 21-Nov-2012 15:53 9.3M
gc5Base.txt.gz 21-Nov-2012 15:50 15M
simpleRepeat.txt.gz 21-Nov-2012 15:49 16M
xenoRefFlat.txt.gz 09-Jul-2017 11:56 29M
netMm10.txt.gz 21-Nov-2012 15:50 30M
xenoRefGene.txt.gz 09-Jul-2017 11:56 33M
xenoRefSeqAli.txt.gz 09-Jul-2017 11:57 33M
rmsk.txt.gz 21-Nov-2012 15:49 37M
chainMm10.txt.gz 21-Nov-2012 15:52 45M
quality.txt.gz 21-Nov-2012 15:51 65M
windowmaskerSdust.txt.gz 21-Nov-2012 15:50 90M
chainMm10Link.txt.gz 21-Nov-2012 15:51 253M