This directory contains a dump of the UCSC genome annotation database for
the Feb. 2008 assembly of the guinea pig genome (cavPor3, Broad Institute cavPor3).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the guinea pig genome, see the project website:
http://www.broad.mit.edu/mammals/
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=cavPor3
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/cavPor3/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/cavPor3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/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 cavPor3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql cavPor3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Guinea Pig 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.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
bigFiles.txt.gz 16-Jul-2017 05:33 33
grp.txt.gz 02-Mar-2014 03:40 208
history.txt.gz 05-Jun-2008 13:36 727
hgFindSpec.txt.gz 16-Jul-2017 05:33 916
nscanPep.sql 05-Jun-2008 13:44 1.1K
genscanPep.sql 05-Jun-2008 13:36 1.2K
chromInfo.sql 05-Jun-2008 13:34 1.2K
ensPep.sql 13-Sep-2015 21:22 1.3K
bigFiles.sql 16-Jul-2017 05:33 1.4K
ensemblSource.sql 13-Sep-2015 21:22 1.4K
windowmaskerSdust.sql 05-Jun-2008 13:49 1.4K
grp.sql 02-Mar-2014 03:40 1.4K
ensemblToGeneName.sql 13-Sep-2015 21:27 1.4K
tableDescriptions.sql 16-Jul-2017 05:33 1.4K
chainGalGal3Link.sql 05-Jun-2008 11:25 1.4K
history.sql 05-Jun-2008 13:36 1.4K
ensGtp.sql 13-Sep-2015 21:22 1.4K
genscanSubopt.sql 05-Jun-2008 13:36 1.5K
chainMonDom4Link.sql 05-Jun-2008 12:27 1.5K
chainOryCun2Link.sql 02-May-2010 11:25 1.5K
microsat.sql 23-Aug-2015 11:56 1.5K
gap.sql 05-Jun-2008 13:34 1.5K
cytoBandIdeo.sql 28-Apr-2013 11:40 1.5K
chainRn6Link.sql 26-Mar-2017 17:13 1.5K
chainMm10Link.sql 27-Oct-2013 10:59 1.5K
tableList.sql 16-Jul-2017 05:33 1.5K
chainGalVar1Link.sql 18-Sep-2016 07:11 1.5K
gbLoaded.sql 09-Jul-2017 08:10 1.6K
genscan.sql 05-Jun-2008 13:36 1.6K
chainHg19Link.sql 20-Sep-2009 08:12 1.6K
gold.sql 05-Jun-2008 13:36 1.6K
cpgIslandExt.sql 05-Jun-2008 13:34 1.6K
chainOryCun2.sql 02-May-2010 11:22 1.6K
chainGalGal3.sql 05-Jun-2008 11:25 1.7K
chainMonDom4.sql 05-Jun-2008 12:18 1.7K
tRNAs.sql 22-Apr-2012 20:01 1.7K
chainRn6.sql 26-Mar-2017 17:10 1.7K
chainMm10.sql 27-Oct-2013 10:59 1.7K
refFlat.sql 25-Jun-2017 08:33 1.7K
chainGalVar1.sql 18-Sep-2016 07:08 1.7K
cpgIslandExtUnmasked.sql 01-Jun-2014 09:51 1.7K
gc5Base.sql 05-Jun-2008 13:36 1.7K
quality.sql 05-Jun-2008 13:44 1.7K
xenoRefFlat.sql 09-Jul-2017 08:07 1.7K
hgFindSpec.sql 16-Jul-2017 05:33 1.7K
estOrientInfo.sql 26-Jun-2016 06:05 1.8K
chainHg19.sql 20-Sep-2009 08:28 1.8K
mrnaOrientInfo.sql 21-May-2017 05:53 1.8K
rmsk.sql 05-Jun-2008 13:46 1.9K
nscanGene.sql 05-Jun-2008 13:44 1.9K
nestedRepeats.sql 05-Jun-2008 13:38 1.9K
simpleRepeat.sql 05-Jun-2008 13:49 1.9K
ensGene.sql 13-Sep-2015 21:22 1.9K
refGene.sql 25-Jun-2017 08:33 1.9K
xenoRefGene.sql 09-Jul-2017 08:07 1.9K
augustusGene.sql 26-Jul-2015 11:11 1.9K
netOryCun2.sql 02-May-2010 11:41 2.0K
trackDb.sql 16-Jul-2017 05:33 2.0K
netRn6.sql 26-Mar-2017 17:42 2.1K
netMm10.sql 27-Oct-2013 11:03 2.1K
netGalVar1.sql 18-Sep-2016 07:23 2.1K
all_est.sql 26-Jun-2016 06:05 2.1K
all_mrna.sql 12-Mar-2017 12:54 2.1K
xenoMrna.sql 09-Jul-2017 08:07 2.1K
intronEst.sql 26-Jun-2016 06:05 2.1K
refSeqAli.sql 21-May-2017 05:53 2.1K
xenoRefSeqAli.sql 09-Jul-2017 08:06 2.1K
netGalGal3.sql 05-Jun-2008 13:39 2.2K
netMonDom4.sql 05-Jun-2008 13:43 2.2K
blastHg18KG.sql 20-Dec-2009 10:45 2.3K
netHg19.sql 20-Sep-2009 08:12 2.3K
tableList.txt.gz 16-Jul-2017 05:33 4.0K
tableDescriptions.txt.gz 16-Jul-2017 05:33 5.2K
tRNAs.txt.gz 22-Apr-2012 20:01 11K
cytoBandIdeo.txt.gz 28-Apr-2013 11:40 18K
chromInfo.txt.gz 05-Jun-2008 13:34 18K
mrnaOrientInfo.txt.gz 21-May-2017 05:53 19K
refFlat.txt.gz 25-Jun-2017 08:33 36K
trackDb.txt.gz 16-Jul-2017 05:33 37K
refGene.txt.gz 25-Jun-2017 08:33 40K
refSeqAli.txt.gz 21-May-2017 05:53 42K
all_mrna.txt.gz 12-Mar-2017 12:54 63K
ensemblSource.txt.gz 13-Sep-2015 21:22 77K
gbLoaded.txt.gz 09-Jul-2017 08:10 85K
ensemblToGeneName.txt.gz 13-Sep-2015 21:27 151K
ensGtp.txt.gz 13-Sep-2015 21:22 258K
estOrientInfo.txt.gz 26-Jun-2016 06:05 341K
intronEst.txt.gz 26-Jun-2016 06:05 534K
microsat.txt.gz 23-Aug-2015 11:56 748K
gap.txt.gz 05-Jun-2008 13:34 819K
cpgIslandExt.txt.gz 05-Jun-2008 13:34 820K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 09:51 841K
all_est.txt.gz 26-Jun-2016 06:05 1.1M
gold.txt.gz 05-Jun-2008 13:36 1.1M
ensGene.txt.gz 13-Sep-2015 21:22 2.0M
nscanGene.txt.gz 05-Jun-2008 13:44 2.1M
augustusGene.txt.gz 26-Jul-2015 11:11 2.7M
blastHg18KG.txt.gz 20-Dec-2009 10:45 3.5M
genscan.txt.gz 05-Jun-2008 13:36 4.2M
ensPep.txt.gz 13-Sep-2015 21:22 5.9M
genscanSubopt.txt.gz 05-Jun-2008 13:36 6.4M
nscanPep.txt.gz 05-Jun-2008 13:44 6.8M
nestedRepeats.txt.gz 05-Jun-2008 13:39 9.1M
gc5Base.txt.gz 05-Jun-2008 13:36 11M
netGalGal3.txt.gz 05-Jun-2008 13:39 13M
genscanPep.txt.gz 05-Jun-2008 13:36 15M
simpleRepeat.txt.gz 05-Jun-2008 13:49 16M
chainGalGal3.txt.gz 05-Jun-2008 11:25 27M
xenoRefFlat.txt.gz 09-Jul-2017 08:07 28M
xenoRefSeqAli.txt.gz 09-Jul-2017 08:06 29M
netMonDom4.txt.gz 05-Jun-2008 13:44 30M
xenoRefGene.txt.gz 09-Jul-2017 08:07 31M
quality.txt.gz 05-Jun-2008 13:46 47M
netRn6.txt.gz 26-Mar-2017 17:43 56M
netMm10.txt.gz 27-Oct-2013 11:03 56M
netHg19.txt.gz 20-Sep-2009 08:12 57M
netOryCun2.txt.gz 02-May-2010 11:41 64M
netGalVar1.txt.gz 18-Sep-2016 07:23 65M
chainRn6.txt.gz 26-Mar-2017 17:11 81M
rmsk.txt.gz 05-Jun-2008 13:48 99M
chainMm10.txt.gz 27-Oct-2013 10:59 111M
windowmaskerSdust.txt.gz 05-Jun-2008 13:51 138M
chainGalGal3Link.txt.gz 05-Jun-2008 11:28 191M
xenoMrna.txt.gz 09-Jul-2017 08:09 304M
chainMonDom4.txt.gz 05-Jun-2008 12:22 385M
chainOryCun2.txt.gz 02-May-2010 11:23 518M
chainHg19.txt.gz 20-Sep-2009 08:30 570M
chainRn6Link.txt.gz 26-Mar-2017 17:21 607M
chainGalVar1.txt.gz 18-Sep-2016 07:09 701M
chainMm10Link.txt.gz 27-Oct-2013 11:00 706M
chainMonDom4Link.txt.gz 05-Jun-2008 12:49 1.8G
chainOryCun2Link.txt.gz 02-May-2010 11:30 2.0G
chainHg19Link.txt.gz 20-Sep-2009 08:17 2.1G
chainGalVar1Link.txt.gz 18-Sep-2016 07:14 2.1G