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 2024-11-24 03:24 73
bigFiles.sql 2024-11-24 03:24 1.4K
tableList.txt.gz 2024-11-24 03:24 4.8K
tableList.sql 2024-11-24 03:24 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 7.3K
tableDescriptions.sql 2024-11-23 02:03 1.4K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
hgFindSpec.sql 2024-01-31 15:13 1.8K
trackDb.txt.gz 2024-01-31 15:13 57K
trackDb.sql 2024-01-31 15:13 2.1K
ensPep.txt.gz 2021-05-25 14:25 8.2M
ensPep.sql 2021-05-25 14:25 1.3K
ensemblSource.txt.gz 2021-05-25 14:25 105K
ensemblSource.sql 2021-05-25 14:25 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:23 171K
ensemblToGeneName.sql 2021-05-25 14:23 1.4K
ensGtp.txt.gz 2021-05-25 14:23 348K
ensGtp.sql 2021-05-25 14:23 1.4K
ensGene.txt.gz 2021-05-25 14:23 2.4M
ensGene.sql 2021-05-25 14:23 1.9K
netMm39.txt.gz 2020-11-26 02:59 56M
netMm39.sql 2020-11-26 02:59 2.1K
chainMm39Link.txt.gz 2020-11-26 02:56 506M
chainMm39Link.sql 2020-11-26 02:56 1.6K
chainMm39.txt.gz 2020-11-26 02:53 62M
chainMm39.sql 2020-11-26 02:53 1.7K
gbLoaded.txt.gz 2020-08-18 13:30 113K
gbLoaded.sql 2020-08-18 13:30 1.6K
xenoRefSeqAli.txt.gz 2020-08-18 13:30 35M
xenoRefSeqAli.sql 2020-08-18 13:30 2.1K
xenoRefFlat.txt.gz 2020-08-18 13:30 32M
xenoRefFlat.sql 2020-08-18 13:30 1.7K
xenoRefGene.txt.gz 2020-08-18 13:30 35M
xenoRefGene.sql 2020-08-18 13:30 2.0K
refFlat.txt.gz 2020-08-18 13:15 37K
refFlat.sql 2020-08-18 13:15 1.7K
refGene.txt.gz 2020-08-18 13:15 40K
refGene.sql 2020-08-18 13:15 1.9K
xenoMrna.txt.gz 2020-08-18 13:10 328M
xenoMrna.sql 2020-08-18 13:10 2.1K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 681K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.8M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.2M
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.3M
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 40K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 255K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.8M
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
mrnaOrientInfo.txt.gz 2020-05-06 01:22 101K
mrnaOrientInfo.sql 2020-05-06 01:22 1.8K
all_mrna.txt.gz 2020-05-06 01:22 298K
all_mrna.sql 2020-05-06 01:22 2.1K
refSeqAli.txt.gz 2018-04-08 05:33 43K
refSeqAli.sql 2018-04-08 05:33 2.1K
ucscToRefSeq.txt.gz 2018-02-18 05:44 25K
ucscToRefSeq.sql 2018-02-18 05:44 1.4K
chromAlias.txt.gz 2018-02-18 05:44 29K
chromAlias.sql 2018-02-18 05:44 1.4K
netRn6.txt.gz 2017-03-26 17:43 56M
netRn6.sql 2017-03-26 17:42 2.1K
chainRn6Link.txt.gz 2017-03-26 17:21 607M
chainRn6Link.sql 2017-03-26 17:13 1.5K
chainRn6.txt.gz 2017-03-26 17:11 81M
chainRn6.sql 2017-03-26 17:10 1.7K
netGalVar1.txt.gz 2016-09-18 07:23 65M
netGalVar1.sql 2016-09-18 07:23 2.1K
chainGalVar1Link.txt.gz 2016-09-18 07:14 2.1G
chainGalVar1Link.sql 2016-09-18 07:11 1.5K
chainGalVar1.txt.gz 2016-09-18 07:09 701M
chainGalVar1.sql 2016-09-18 07:08 1.7K
intronEst.txt.gz 2016-06-26 06:05 534K
intronEst.sql 2016-06-26 06:05 2.1K
estOrientInfo.txt.gz 2016-06-26 06:05 341K
estOrientInfo.sql 2016-06-26 06:05 1.8K
all_est.txt.gz 2016-06-26 06:05 1.1M
all_est.sql 2016-06-26 06:05 2.1K
microsat.txt.gz 2015-08-23 11:56 748K
microsat.sql 2015-08-23 11:56 1.5K
augustusGene.txt.gz 2015-07-26 11:11 2.7M
augustusGene.sql 2015-07-26 11:11 1.9K
cpgIslandExtUnmasked.txt.gz 2014-06-01 09:51 841K
cpgIslandExtUnmasked.sql 2014-06-01 09:51 1.7K
grp.txt.gz 2014-03-02 03:40 208
grp.sql 2014-03-02 03:40 1.4K
netMm10.txt.gz 2013-10-27 11:03 56M
netMm10.sql 2013-10-27 11:03 2.1K
chainMm10Link.txt.gz 2013-10-27 11:00 706M
chainMm10Link.sql 2013-10-27 10:59 1.5K
chainMm10.txt.gz 2013-10-27 10:59 111M
chainMm10.sql 2013-10-27 10:59 1.7K
cytoBandIdeo.txt.gz 2013-04-28 11:40 18K
cytoBandIdeo.sql 2013-04-28 11:40 1.5K
tRNAs.txt.gz 2012-04-22 20:01 11K
tRNAs.sql 2012-04-22 20:01 1.7K
netOryCun2.txt.gz 2010-05-02 11:41 64M
netOryCun2.sql 2010-05-02 11:41 2.0K
chainOryCun2Link.txt.gz 2010-05-02 11:30 2.0G
chainOryCun2Link.sql 2010-05-02 11:25 1.5K
chainOryCun2.txt.gz 2010-05-02 11:23 518M
chainOryCun2.sql 2010-05-02 11:22 1.6K
blastHg18KG.txt.gz 2009-12-20 10:45 3.5M
blastHg18KG.sql 2009-12-20 10:45 2.3K
chainHg19.txt.gz 2009-09-20 08:30 570M
chainHg19.sql 2009-09-20 08:28 1.8K
chainHg19Link.txt.gz 2009-09-20 08:17 2.1G
chainHg19Link.sql 2009-09-20 08:12 1.6K
netHg19.txt.gz 2009-09-20 08:12 57M
netHg19.sql 2009-09-20 08:12 2.3K
windowmaskerSdust.txt.gz 2008-06-05 13:51 138M
windowmaskerSdust.sql 2008-06-05 13:49 1.4K
simpleRepeat.txt.gz 2008-06-05 13:49 16M
simpleRepeat.sql 2008-06-05 13:49 1.9K
rmsk.txt.gz 2008-06-05 13:48 99M
rmsk.sql 2008-06-05 13:46 1.9K
quality.txt.gz 2008-06-05 13:46 47M
quality.sql 2008-06-05 13:44 1.7K
nscanPep.txt.gz 2008-06-05 13:44 6.8M
nscanPep.sql 2008-06-05 13:44 1.1K
nscanGene.txt.gz 2008-06-05 13:44 2.1M
nscanGene.sql 2008-06-05 13:44 1.9K
netMonDom4.txt.gz 2008-06-05 13:44 30M
netMonDom4.sql 2008-06-05 13:43 2.2K
netGalGal3.txt.gz 2008-06-05 13:39 13M
netGalGal3.sql 2008-06-05 13:39 2.2K
nestedRepeats.txt.gz 2008-06-05 13:39 9.1M
nestedRepeats.sql 2008-06-05 13:38 1.9K
history.txt.gz 2008-06-05 13:36 727
history.sql 2008-06-05 13:36 1.4K
gold.txt.gz 2008-06-05 13:36 1.1M
gold.sql 2008-06-05 13:36 1.6K
genscanSubopt.txt.gz 2008-06-05 13:36 6.4M
genscanSubopt.sql 2008-06-05 13:36 1.5K
genscanPep.txt.gz 2008-06-05 13:36 15M
genscanPep.sql 2008-06-05 13:36 1.2K
genscan.txt.gz 2008-06-05 13:36 4.2M
genscan.sql 2008-06-05 13:36 1.6K
gc5Base.txt.gz 2008-06-05 13:36 11M
gc5Base.sql 2008-06-05 13:36 1.7K
gap.txt.gz 2008-06-05 13:34 819K
gap.sql 2008-06-05 13:34 1.5K
cpgIslandExt.txt.gz 2008-06-05 13:34 820K
cpgIslandExt.sql 2008-06-05 13:34 1.6K
chromInfo.txt.gz 2008-06-05 13:34 18K
chromInfo.sql 2008-06-05 13:34 1.2K
chainMonDom4Link.txt.gz 2008-06-05 12:49 1.8G
chainMonDom4Link.sql 2008-06-05 12:27 1.5K
chainMonDom4.txt.gz 2008-06-05 12:22 385M
chainMonDom4.sql 2008-06-05 12:18 1.7K
chainGalGal3Link.txt.gz 2008-06-05 11:28 191M
chainGalGal3Link.sql 2008-06-05 11:25 1.4K
chainGalGal3.txt.gz 2008-06-05 11:25 27M
chainGalGal3.sql 2008-06-05 11:25 1.7K