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
xenoRefGene.sql 2020-08-22 14:19 2.0K
xenoRefGene.txt.gz 2020-08-22 14:19 37M
xenoRefFlat.sql 2020-08-22 14:19 1.7K
xenoRefFlat.txt.gz 2020-08-22 14:19 33M
xenoRefSeqAli.sql 2020-08-22 14:19 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 14:19 40M
gbLoaded.sql 2020-08-22 14:19 1.6K
gbLoaded.txt.gz 2020-08-22 14:19 30K
trackDb.sql 2023-03-28 13:51 2.1K
trackDb.txt.gz 2023-03-28 13:51 20K
hgFindSpec.sql 2023-03-28 13:51 1.8K
hgFindSpec.txt.gz 2023-03-28 13:51 747
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 5.5K
tableList.sql 2024-11-17 03:20 1.6K
tableList.txt.gz 2024-11-17 03:20 2.3K
bigFiles.sql 2024-11-17 03:20 1.4K
bigFiles.txt.gz 2024-11-17 03:20 33