This directory contains a dump of the UCSC genome annotation database for
the Mar. 2007 assembly of the lamprey genome (UCSC version petMar1,
WUSTL v.3.0, March 2007). The annotations were generated by UCSC and
collaborators worldwide.
This assembly was produced by the Genome Sequencing Center at the
Washington University in St. Louis School of Medicine.
For more information on the lamprey genome, see the project website at
http://genome.wustl.edu/genome.cgi?GENOME=Petromyzon%20marinus.
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=petMar1
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/petMar1/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/petMar1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/petMar1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar1/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 petMar1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql petMar1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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All the files and tables in this directory are freely usable for any purpose.
The Lamprey sequence is made freely available before scientific publication
by the Genome Sequencing Center, Washington University in St. Louis School of
Medicine. Please see the WUSTL data use policy at http://genome.wustl.edu/data.cgi
for usage restrictions and citation information.
Name Last modified Size Description
Parent Directory -
bigFiles.txt.gz 2024-12-08 03:32 33
bigFiles.sql 2024-12-08 03:32 1.4K
tableList.txt.gz 2024-12-08 03:32 3.2K
tableList.sql 2024-12-08 03:32 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 5.7K
tableDescriptions.sql 2024-12-07 02:03 1.5K
hgFindSpec.txt.gz 2023-03-28 13:52 663
hgFindSpec.sql 2023-03-28 13:52 1.8K
trackDb.txt.gz 2023-03-28 13:52 38K
trackDb.sql 2023-03-28 13:52 2.1K
gbLoaded.txt.gz 2020-08-22 22:56 104K
gbLoaded.sql 2020-08-22 22:56 1.6K
xenoRefSeqAli.txt.gz 2020-08-22 22:53 16M
xenoRefSeqAli.sql 2020-08-22 22:53 2.1K
xenoRefFlat.txt.gz 2020-08-22 22:53 13M
xenoRefFlat.sql 2020-08-22 22:53 1.7K
xenoRefGene.txt.gz 2020-08-22 22:40 14M
xenoRefGene.sql 2020-08-22 22:40 2.0K
mrnaOrientInfo.txt.gz 2020-08-22 22:19 43K
mrnaOrientInfo.sql 2020-08-22 22:19 1.8K
xenoMrna.txt.gz 2020-08-22 22:19 152M
xenoMrna.sql 2020-08-22 22:19 2.1K
all_mrna.txt.gz 2020-08-22 22:18 155K
all_mrna.sql 2020-08-22 22:18 2.1K
microsat.txt.gz 2015-08-24 00:19 131
microsat.sql 2015-08-24 00:19 1.5K
augustusGene.txt.gz 2015-07-26 17:21 2.3M
augustusGene.sql 2015-07-26 17:21 1.9K
grp.txt.gz 2014-03-02 04:14 199
grp.sql 2014-03-02 04:14 1.4K
tRNAs.txt.gz 2012-04-23 09:28 53K
tRNAs.sql 2012-04-23 09:28 1.7K
intronEst.txt.gz 2011-04-18 08:53 1.7M
intronEst.sql 2011-04-18 08:53 2.0K
all_est.txt.gz 2011-04-18 08:53 4.7M
all_est.sql 2011-04-18 08:53 2.0K
estOrientInfo.txt.gz 2011-04-18 08:47 1.2M
estOrientInfo.sql 2011-04-18 08:47 1.7K
blastHg18KG.txt.gz 2009-12-20 15:36 1.4M
blastHg18KG.sql 2009-12-20 15:36 2.3K
chainHg19.txt.gz 2009-10-11 08:48 14M
chainHg19.sql 2009-10-11 08:48 1.8K
netHg19.txt.gz 2009-10-11 08:48 3.3M
netHg19.sql 2009-10-11 08:48 2.3K
chainHg19Link.txt.gz 2009-10-11 08:48 44M
chainHg19Link.sql 2009-10-11 08:48 1.5K
quality.txt.gz 2008-11-30 12:36 22M
quality.sql 2008-11-30 12:36 1.7K
netOryLat2.txt.gz 2008-11-16 12:16 4.5M
netOryLat2.sql 2008-11-16 12:16 2.2K
chainOryLat2Link.txt.gz 2008-11-16 12:15 79M
chainOryLat2Link.sql 2008-11-16 12:15 1.4K
chainOryLat2.txt.gz 2008-11-16 12:15 23M
chainOryLat2.sql 2008-11-16 12:15 1.7K
windowmaskerSdust.txt.gz 2008-06-09 14:04 44M
windowmaskerSdust.sql 2008-06-09 14:03 1.4K
simpleRepeat.txt.gz 2008-06-09 14:03 17M
simpleRepeat.sql 2008-06-09 14:03 1.9K
phastConsElements6way.txt.gz 2008-06-09 14:02 801K
phastConsElements6way.sql 2008-06-09 14:02 1.4K
phastCons6way.txt.gz 2008-06-09 14:02 2.3M
phastCons6way.sql 2008-06-09 14:02 1.7K
netMm9.txt.gz 2008-06-09 14:02 3.3M
netMm9.sql 2008-06-09 14:02 2.2K
netGalGal3.txt.gz 2008-06-09 14:02 3.0M
netGalGal3.sql 2008-06-09 14:02 2.2K
netBraFlo1.txt.gz 2008-06-09 14:02 2.8M
netBraFlo1.sql 2008-06-09 14:02 2.2K
nestedRepeats.txt.gz 2008-06-09 14:02 347K
nestedRepeats.sql 2008-06-09 14:02 1.9K
multiz6wayFrames.txt.gz 2008-06-09 14:02 4.7M
multiz6wayFrames.sql 2008-06-09 14:02 1.7K
multiz6way.txt.gz 2008-06-09 14:02 4.0M
multiz6way.sql 2008-06-09 14:02 1.4K
history.txt.gz 2008-06-09 14:01 745
history.sql 2008-06-09 14:01 1.4K
gold.txt.gz 2008-06-09 14:01 3.9M
gold.sql 2008-06-09 14:01 1.6K
gc5Base.txt.gz 2008-06-09 14:01 5.9M
gc5Base.sql 2008-06-09 14:01 1.7K
gap.txt.gz 2008-06-09 13:59 2.1M
gap.sql 2008-06-09 13:59 1.5K
extFile.txt.gz 2008-06-09 13:59 101
extFile.sql 2008-06-09 13:59 1.3K
chromInfo.txt.gz 2008-06-09 13:59 517K
chromInfo.sql 2008-06-09 13:59 1.2K
chainMm9Link.txt.gz 2008-06-09 13:57 32M
chainMm9Link.sql 2008-06-09 13:57 1.4K
chainGalGal3Link.txt.gz 2008-06-09 13:56 31M
chainGalGal3Link.sql 2008-06-09 13:55 1.4K
chainGalGal3.txt.gz 2008-06-09 13:55 11M
chainGalGal3.sql 2008-06-09 13:55 1.7K
chainBraFlo1Link.txt.gz 2008-06-09 13:55 43M
chainBraFlo1Link.sql 2008-06-09 13:54 1.4K
chainMm9.txt.gz 2008-06-09 13:54 11M
chainMm9.sql 2008-06-09 13:54 1.6K
chainBraFlo1.txt.gz 2008-06-09 13:54 9.2M
chainBraFlo1.sql 2008-06-09 13:54 1.7K