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.
---------------------------------------------------------------
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;'
---------------------------------------------------------------
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 2024-11-24 03:26 33
extFile.txt.gz 2008-06-09 13:59 101
microsat.txt.gz 2015-08-24 00:19 131
grp.txt.gz 2014-03-02 04:14 199
hgFindSpec.txt.gz 2023-03-28 13:52 663
history.txt.gz 2008-06-09 14:01 745
chromInfo.sql 2008-06-09 13:59 1.2K
extFile.sql 2008-06-09 13:59 1.3K
bigFiles.sql 2024-11-24 03:26 1.4K
windowmaskerSdust.sql 2008-06-09 14:03 1.4K
grp.sql 2014-03-02 04:14 1.4K
chainMm9Link.sql 2008-06-09 13:57 1.4K
multiz6way.sql 2008-06-09 14:02 1.4K
chainBraFlo1Link.sql 2008-06-09 13:54 1.4K
chainGalGal3Link.sql 2008-06-09 13:55 1.4K
chainOryLat2Link.sql 2008-11-16 12:15 1.4K
history.sql 2008-06-09 14:01 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
phastConsElements6way.sql 2008-06-09 14:02 1.4K
microsat.sql 2015-08-24 00:19 1.5K
gap.sql 2008-06-09 13:59 1.5K
chainHg19Link.sql 2009-10-11 08:48 1.5K
tableList.sql 2024-11-24 03:26 1.6K
gold.sql 2008-06-09 14:01 1.6K
gbLoaded.sql 2020-08-22 22:56 1.6K
chainMm9.sql 2008-06-09 13:54 1.6K
chainBraFlo1.sql 2008-06-09 13:54 1.7K
chainGalGal3.sql 2008-06-09 13:55 1.7K
chainOryLat2.sql 2008-11-16 12:15 1.7K
multiz6wayFrames.sql 2008-06-09 14:02 1.7K
tRNAs.sql 2012-04-23 09:28 1.7K
estOrientInfo.sql 2011-04-18 08:47 1.7K
gc5Base.sql 2008-06-09 14:01 1.7K
quality.sql 2008-11-30 12:36 1.7K
phastCons6way.sql 2008-06-09 14:02 1.7K
xenoRefFlat.sql 2020-08-22 22:53 1.7K
hgFindSpec.sql 2023-03-28 13:52 1.8K
chainHg19.sql 2009-10-11 08:48 1.8K
mrnaOrientInfo.sql 2020-08-22 22:19 1.8K
nestedRepeats.sql 2008-06-09 14:02 1.9K
simpleRepeat.sql 2008-06-09 14:03 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
xenoRefGene.sql 2020-08-22 22:40 2.0K
all_est.sql 2011-04-18 08:53 2.0K
intronEst.sql 2011-04-18 08:53 2.0K
trackDb.sql 2023-03-28 13:52 2.1K
all_mrna.sql 2020-08-22 22:18 2.1K
xenoMrna.sql 2020-08-22 22:19 2.1K
xenoRefSeqAli.sql 2020-08-22 22:53 2.1K
netMm9.sql 2008-06-09 14:02 2.2K
netBraFlo1.sql 2008-06-09 14:02 2.2K
netGalGal3.sql 2008-06-09 14:02 2.2K
netOryLat2.sql 2008-11-16 12:16 2.2K
blastHg18KG.sql 2009-12-20 15:36 2.3K
netHg19.sql 2009-10-11 08:48 2.3K
tableList.txt.gz 2024-11-24 03:26 3.2K
tableDescriptions.txt.gz 2024-11-23 02:03 5.7K
trackDb.txt.gz 2023-03-28 13:52 38K
mrnaOrientInfo.txt.gz 2020-08-22 22:19 43K
tRNAs.txt.gz 2012-04-23 09:28 53K
gbLoaded.txt.gz 2020-08-22 22:56 104K
all_mrna.txt.gz 2020-08-22 22:18 155K
nestedRepeats.txt.gz 2008-06-09 14:02 347K
chromInfo.txt.gz 2008-06-09 13:59 517K
phastConsElements6way.txt.gz 2008-06-09 14:02 801K
estOrientInfo.txt.gz 2011-04-18 08:47 1.2M
blastHg18KG.txt.gz 2009-12-20 15:36 1.4M
intronEst.txt.gz 2011-04-18 08:53 1.7M
gap.txt.gz 2008-06-09 13:59 2.1M
phastCons6way.txt.gz 2008-06-09 14:02 2.3M
augustusGene.txt.gz 2015-07-26 17:21 2.3M
netBraFlo1.txt.gz 2008-06-09 14:02 2.8M
netGalGal3.txt.gz 2008-06-09 14:02 3.0M
netHg19.txt.gz 2009-10-11 08:48 3.3M
netMm9.txt.gz 2008-06-09 14:02 3.3M
gold.txt.gz 2008-06-09 14:01 3.9M
multiz6way.txt.gz 2008-06-09 14:02 4.0M
netOryLat2.txt.gz 2008-11-16 12:16 4.5M
multiz6wayFrames.txt.gz 2008-06-09 14:02 4.7M
all_est.txt.gz 2011-04-18 08:53 4.7M
gc5Base.txt.gz 2008-06-09 14:01 5.9M
chainBraFlo1.txt.gz 2008-06-09 13:54 9.2M
chainGalGal3.txt.gz 2008-06-09 13:55 11M
chainMm9.txt.gz 2008-06-09 13:54 11M
xenoRefFlat.txt.gz 2020-08-22 22:53 13M
chainHg19.txt.gz 2009-10-11 08:48 14M
xenoRefGene.txt.gz 2020-08-22 22:40 14M
xenoRefSeqAli.txt.gz 2020-08-22 22:53 16M
simpleRepeat.txt.gz 2008-06-09 14:03 17M
quality.txt.gz 2008-11-30 12:36 22M
chainOryLat2.txt.gz 2008-11-16 12:15 23M
chainGalGal3Link.txt.gz 2008-06-09 13:56 31M
chainMm9Link.txt.gz 2008-06-09 13:57 32M
chainBraFlo1Link.txt.gz 2008-06-09 13:55 43M
windowmaskerSdust.txt.gz 2008-06-09 14:04 44M
chainHg19Link.txt.gz 2009-10-11 08:48 44M
chainOryLat2Link.txt.gz 2008-11-16 12:15 79M
xenoMrna.txt.gz 2020-08-22 22:19 152M