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 2024-04-14 03:30 73
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2008-06-05 13:36 727
nscanPep.sql 2008-06-05 13:44 1.1K
genscanPep.sql 2008-06-05 13:36 1.2K
chromInfo.sql 2008-06-05 13:34 1.2K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K
ensPep.sql 2021-05-25 14:25 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ensemblSource.sql 2021-05-25 14:25 1.4K
windowmaskerSdust.sql 2008-06-05 13:49 1.4K
grp.sql 2014-03-02 03:40 1.4K
bigFiles.sql 2024-04-14 03:30 1.4K
ensemblToGeneName.sql 2021-05-25 14:23 1.4K
chainGalGal3Link.sql 2008-06-05 11:25 1.4K
chromAlias.sql 2018-02-18 05:44 1.4K
history.sql 2008-06-05 13:36 1.4K
ucscToRefSeq.sql 2018-02-18 05:44 1.4K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
ensGtp.sql 2021-05-25 14:23 1.4K
genscanSubopt.sql 2008-06-05 13:36 1.5K
tableDescriptions.sql 2024-04-13 02:03 1.5K
chainMonDom4Link.sql 2008-06-05 12:27 1.5K
chainOryCun2Link.sql 2010-05-02 11:25 1.5K
microsat.sql 2015-08-23 11:56 1.5K
gap.sql 2008-06-05 13:34 1.5K
cytoBandIdeo.sql 2013-04-28 11:40 1.5K
chainRn6Link.sql 2017-03-26 17:13 1.5K
chainMm10Link.sql 2013-10-27 10:59 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
chainGalVar1Link.sql 2016-09-18 07:11 1.5K
chainMm39Link.sql 2020-11-26 02:56 1.6K
genscan.sql 2008-06-05 13:36 1.6K
chainHg19Link.sql 2009-09-20 08:12 1.6K
tableList.sql 2024-04-14 03:30 1.6K
gold.sql 2008-06-05 13:36 1.6K
gbLoaded.sql 2020-08-18 13:30 1.6K
cpgIslandExt.sql 2008-06-05 13:34 1.6K
chainOryCun2.sql 2010-05-02 11:22 1.6K
chainGalGal3.sql 2008-06-05 11:25 1.7K
chainMonDom4.sql 2008-06-05 12:18 1.7K
tRNAs.sql 2012-04-22 20:01 1.7K
chainRn6.sql 2017-03-26 17:10 1.7K
chainMm10.sql 2013-10-27 10:59 1.7K
chainGalVar1.sql 2016-09-18 07:08 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 09:51 1.7K
gc5Base.sql 2008-06-05 13:36 1.7K
quality.sql 2008-06-05 13:44 1.7K
chainMm39.sql 2020-11-26 02:53 1.7K
refFlat.sql 2020-08-18 13:15 1.7K
xenoRefFlat.sql 2020-08-18 13:30 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
estOrientInfo.sql 2016-06-26 06:05 1.8K
chainHg19.sql 2009-09-20 08:28 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
mrnaOrientInfo.sql 2020-05-06 01:22 1.8K
rmsk.sql 2008-06-05 13:46 1.9K
nscanGene.sql 2008-06-05 13:44 1.9K
nestedRepeats.sql 2008-06-05 13:38 1.9K
simpleRepeat.sql 2008-06-05 13:49 1.9K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
augustusGene.sql 2015-07-26 11:11 1.9K
ensGene.sql 2021-05-25 14:23 1.9K
refGene.sql 2020-08-18 13:15 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
xenoRefGene.sql 2020-08-18 13:30 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
netOryCun2.sql 2010-05-02 11:41 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netRn6.sql 2017-03-26 17:42 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
netMm10.sql 2013-10-27 11:03 2.1K
netGalVar1.sql 2016-09-18 07:23 2.1K
all_est.sql 2016-06-26 06:05 2.1K
intronEst.sql 2016-06-26 06:05 2.1K
refSeqAli.sql 2018-04-08 05:33 2.1K
netMm39.sql 2020-11-26 02:59 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
all_mrna.sql 2020-05-06 01:22 2.1K
xenoMrna.sql 2020-08-18 13:10 2.1K
xenoRefSeqAli.sql 2020-08-18 13:30 2.1K
netGalGal3.sql 2008-06-05 13:39 2.2K
netMonDom4.sql 2008-06-05 13:43 2.2K
blastHg18KG.sql 2009-12-20 10:45 2.3K
netHg19.sql 2009-09-20 08:12 2.3K
tableList.txt.gz 2024-04-14 03:30 4.9K
tableDescriptions.txt.gz 2024-04-13 02:03 7.3K
tRNAs.txt.gz 2012-04-22 20:01 11K
cytoBandIdeo.txt.gz 2013-04-28 11:40 18K
chromInfo.txt.gz 2008-06-05 13:34 18K
ucscToRefSeq.txt.gz 2018-02-18 05:44 25K
chromAlias.txt.gz 2018-02-18 05:44 29K
refFlat.txt.gz 2020-08-18 13:15 37K
refGene.txt.gz 2020-08-18 13:15 40K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 40K
trackDb_pushedout.txt.gz 2023-12-05 13:51 41K
refSeqAli.txt.gz 2018-04-08 05:33 43K
trackDb.txt.gz 2024-01-31 15:13 57K
mrnaOrientInfo.txt.gz 2020-05-06 01:22 101K
ensemblSource.txt.gz 2021-05-25 14:25 105K
gbLoaded.txt.gz 2020-08-18 13:30 113K
ensemblToGeneName.txt.gz 2021-05-25 14:23 171K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 255K
all_mrna.txt.gz 2020-05-06 01:22 298K
estOrientInfo.txt.gz 2016-06-26 06:05 341K
ensGtp.txt.gz 2021-05-25 14:23 348K
intronEst.txt.gz 2016-06-26 06:05 534K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 681K
microsat.txt.gz 2015-08-23 11:56 748K
gap.txt.gz 2008-06-05 13:34 819K
cpgIslandExt.txt.gz 2008-06-05 13:34 820K
cpgIslandExtUnmasked.txt.gz 2014-06-01 09:51 841K
all_est.txt.gz 2016-06-26 06:05 1.1M
gold.txt.gz 2008-06-05 13:36 1.1M
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.3M
nscanGene.txt.gz 2008-06-05 13:44 2.1M
ensGene.txt.gz 2021-05-25 14:23 2.4M
augustusGene.txt.gz 2015-07-26 11:11 2.7M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.8M
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.8M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 3.3M
blastHg18KG.txt.gz 2009-12-20 10:45 3.5M
genscan.txt.gz 2008-06-05 13:36 4.2M
genscanSubopt.txt.gz 2008-06-05 13:36 6.4M
nscanPep.txt.gz 2008-06-05 13:44 6.8M
ensPep.txt.gz 2021-05-25 14:25 8.2M
nestedRepeats.txt.gz 2008-06-05 13:39 9.1M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.2M
gc5Base.txt.gz 2008-06-05 13:36 11M
netGalGal3.txt.gz 2008-06-05 13:39 13M
genscanPep.txt.gz 2008-06-05 13:36 15M
simpleRepeat.txt.gz 2008-06-05 13:49 16M
chainGalGal3.txt.gz 2008-06-05 11:25 27M
netMonDom4.txt.gz 2008-06-05 13:44 30M
xenoRefFlat.txt.gz 2020-08-18 13:30 32M
xenoRefGene.txt.gz 2020-08-18 13:30 35M
xenoRefSeqAli.txt.gz 2020-08-18 13:30 35M
quality.txt.gz 2008-06-05 13:46 47M
netRn6.txt.gz 2017-03-26 17:43 56M
netMm39.txt.gz 2020-11-26 02:59 56M
netMm10.txt.gz 2013-10-27 11:03 56M
netHg19.txt.gz 2009-09-20 08:12 57M
chainMm39.txt.gz 2020-11-26 02:53 62M
netOryCun2.txt.gz 2010-05-02 11:41 64M
netGalVar1.txt.gz 2016-09-18 07:23 65M
chainRn6.txt.gz 2017-03-26 17:11 81M
rmsk.txt.gz 2008-06-05 13:48 99M
chainMm10.txt.gz 2013-10-27 10:59 111M
windowmaskerSdust.txt.gz 2008-06-05 13:51 138M
chainGalGal3Link.txt.gz 2008-06-05 11:28 191M
xenoMrna.txt.gz 2020-08-18 13:10 328M
chainMonDom4.txt.gz 2008-06-05 12:22 385M
chainMm39Link.txt.gz 2020-11-26 02:56 506M
chainOryCun2.txt.gz 2010-05-02 11:23 518M
chainHg19.txt.gz 2009-09-20 08:30 570M
chainRn6Link.txt.gz 2017-03-26 17:21 607M
chainGalVar1.txt.gz 2016-09-18 07:09 701M
chainMm10Link.txt.gz 2013-10-27 11:00 706M
chainMonDom4Link.txt.gz 2008-06-05 12:49 1.8G
chainOryCun2Link.txt.gz 2010-05-02 11:30 2.0G
chainHg19Link.txt.gz 2009-09-20 08:17 2.1G
chainGalVar1Link.txt.gz 2016-09-18 07:14 2.1G