This directory contains a dump of the UCSC genome annotation database for the
May 2012 (OchPri3.0/ochPri3) assembly of the pika genome
(ochPri3, Broad Institute) .
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/681538
http://www.ncbi.nlm.nih.gov/bioproject/193497
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=ochPri3
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/ochPri3/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/ochPri3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ochPri3/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 ochPri3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql ochPri3 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
all_mrna.sql 2019-03-17 11:38 2.1K
all_mrna.txt.gz 2019-03-17 11:38 434
augustusGene.sql 2015-07-26 17:04 1.9K
augustusGene.txt.gz 2015-07-26 17:04 2.2M
bigFiles.sql 2024-12-08 03:35 1.4K
bigFiles.txt.gz 2024-12-08 03:35 94
chainHg19.sql 2014-07-14 14:37 1.7K
chainHg19.txt.gz 2014-07-14 14:37 123M
chainHg19Link.sql 2014-07-14 14:37 1.5K
chainHg19Link.txt.gz 2014-07-14 14:38 572M
chainMm39.sql 2020-11-25 23:35 1.7K
chainMm39.txt.gz 2020-11-25 23:35 38M
chainMm39Link.sql 2020-11-25 23:37 1.6K
chainMm39Link.txt.gz 2020-11-25 23:37 284M
chromAlias.sql 2016-10-20 16:13 1.4K
chromAlias.txt.gz 2016-10-20 16:13 100K
chromInfo.sql 2014-07-14 14:40 1.4K
chromInfo.txt.gz 2014-07-14 14:40 48K
cpgIslandExt.sql 2014-07-14 14:40 1.7K
cpgIslandExt.txt.gz 2014-07-14 14:40 603K
cpgIslandExtUnmasked.sql 2014-07-14 14:40 1.7K
cpgIslandExtUnmasked.txt.gz 2014-07-14 14:40 898K
cytoBandIdeo.sql 2014-07-14 14:40 1.5K
cytoBandIdeo.txt.gz 2014-07-14 14:40 48K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
gap.sql 2014-07-14 14:40 1.6K
gap.txt.gz 2014-07-14 14:40 1.7M
gbLoaded.sql 2020-08-19 21:58 1.6K
gbLoaded.txt.gz 2020-08-19 21:58 24K
gc5BaseBw.sql 2014-07-14 14:41 1.3K
gc5BaseBw.txt.gz 2014-07-14 14:41 63
genscan.sql 2014-07-14 14:41 1.7K
genscan.txt.gz 2014-07-14 14:41 3.2M
gold.sql 2014-07-14 14:40 1.7K
gold.txt.gz 2014-07-14 14:40 2.2M
grp.sql 2014-08-03 11:48 1.3K
grp.txt.gz 2014-08-03 11:48 199
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.0K
history.sql 2014-07-14 14:40 1.6K
history.txt.gz 2014-07-14 14:40 461
microsat.sql 2015-08-23 22:31 1.5K
microsat.txt.gz 2015-08-23 22:31 345K
mrnaOrientInfo.sql 2019-03-17 11:37 1.8K
mrnaOrientInfo.txt.gz 2019-03-17 11:37 181
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.1M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 158K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 1.4K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 851K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 6.5M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.1M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.3M
nestedRepeats.sql 2014-07-14 14:36 1.9K
nestedRepeats.txt.gz 2014-07-14 14:36 5.1M
netHg19.sql 2014-07-14 14:37 2.1K
netHg19.txt.gz 2014-07-14 14:37 45M
netMm39.sql 2020-11-25 23:39 2.1K
netMm39.txt.gz 2020-11-25 23:39 34M
rmsk.sql 2014-07-14 14:40 1.9K
rmsk.txt.gz 2014-07-14 14:40 72M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 399K
simpleRepeat.sql 2014-07-14 14:41 1.9K
simpleRepeat.txt.gz 2014-07-14 14:41 10M
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 6.0K
tableList.sql 2024-12-08 03:35 1.6K
tableList.txt.gz 2024-12-08 03:35 2.8K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 43K
ucscToINSDC.sql 2014-07-14 14:41 1.4K
ucscToINSDC.txt.gz 2014-07-14 14:41 72K
windowmaskerSdust.sql 2014-07-14 14:41 1.5K
windowmaskerSdust.txt.gz 2014-07-14 14:41 101M
xenoRefFlat.sql 2020-08-19 21:58 1.7K
xenoRefFlat.txt.gz 2020-08-19 21:58 28M
xenoRefGene.sql 2020-08-19 21:58 2.0K
xenoRefGene.txt.gz 2020-08-19 21:58 31M
xenoRefSeqAli.sql 2020-08-19 21:58 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 21:58 30M