This directory contains a dump of the UCSC genome annotation database for
the Mar. 2006 assembly of the lancelet genome (UCSC version braFlo1;
JGI v.1.0, March 2006). The annotations were generated by UCSC and
collaborators worldwide.
This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the lancelet genome, see the project website at
http://genome.jgi-psf.org/Brafl1/Brafl1.info.html.
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=braFlo1
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/braFlo1/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/braFlo1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/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 braFlo1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql braFlo1 --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 lancelet sequence is made freely available before scientific publication
by the JGI. Please see the JGI data release policy at
http://genome.jgi-psf.org/Brafl1/Brafl1.download.html for usage restrictions
and citation information.
Name Last modified Size Description
Parent Directory -
blastHg18KG.sql 2008-06-09 13:44 2.1K
blastHg18KG.txt.gz 2008-06-09 13:44 2.2M
chrM_chainGalGal3.sql 2008-06-09 13:44 1.7K
chrM_chainGalGal3.txt.gz 2008-06-09 13:44 256
chrM_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrM_chainGalGal3Link.txt.gz 2008-06-09 13:44 2.1K
chrM_chainHg18.sql 2008-06-09 13:44 1.7K
chrM_chainHg18.txt.gz 2008-06-09 13:44 6.0K
chrM_chainHg18Link.sql 2008-06-09 13:44 1.4K
chrM_chainHg18Link.txt.gz 2008-06-09 13:44 71K
chrM_chainMm9.sql 2008-06-09 13:44 1.6K
chrM_chainMm9.txt.gz 2008-06-09 13:44 1.0K
chrM_chainMm9Link.sql 2008-06-09 13:44 1.4K
chrM_chainMm9Link.txt.gz 2008-06-09 13:44 7.2K
chrM_chainPetMar1.sql 2008-06-09 13:44 1.7K
chrM_chainPetMar1.txt.gz 2008-06-09 13:44 882
chrM_chainPetMar1Link.sql 2008-06-09 13:44 1.4K
chrM_chainPetMar1Link.txt.gz 2008-06-09 13:44 4.8K
chrM_gap.sql 2008-06-09 13:44 1.5K
chrM_gap.txt.gz 2008-06-09 13:44 33
chrM_gold.sql 2008-06-09 13:44 1.6K
chrM_gold.txt.gz 2008-06-09 13:44 68
chrUn_chainGalGal3.sql 2008-06-09 13:44 1.7K
chrUn_chainGalGal3.txt.gz 2008-06-09 13:44 2.6M
chrUn_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrUn_chainGalGal3Link.txt.gz 2008-06-09 13:44 15M
chrUn_chainHg18.sql 2008-06-09 13:44 1.7K
chrUn_chainHg18.txt.gz 2008-06-09 13:44 6.4M
chrUn_chainHg18Link.sql 2008-06-09 13:45 1.4K
chrUn_chainHg18Link.txt.gz 2008-06-09 13:45 29M
chrUn_chainMm9.sql 2008-06-09 13:45 1.7K
chrUn_chainMm9.txt.gz 2008-06-09 13:45 4.9M
chrUn_chainMm9Link.sql 2008-06-09 13:45 1.4K
chrUn_chainMm9Link.txt.gz 2008-06-09 13:46 23M
chrUn_chainPetMar1.sql 2008-06-09 13:46 1.7K
chrUn_chainPetMar1.txt.gz 2008-06-09 13:46 9.7M
chrUn_chainPetMar1Link.sql 2008-06-09 13:46 1.4K
chrUn_chainPetMar1Link.txt.gz 2008-06-09 13:47 44M
chrUn_gap.sql 2008-06-09 13:47 1.5K
chrUn_gap.txt.gz 2008-06-09 13:47 1.2M
chrUn_gold.sql 2008-06-09 13:47 1.6K
chrUn_gold.txt.gz 2008-06-09 13:47 57K
chromInfo.sql 2008-06-09 13:47 1.2K
chromInfo.txt.gz 2008-06-09 13:47 82
extFile.sql 2008-06-09 13:47 1.3K
extFile.txt.gz 2008-06-09 13:47 133
gc5Base.sql 2008-06-09 13:50 1.7K
gc5Base.txt.gz 2008-06-09 13:50 3.8M
history.sql 2008-06-09 13:50 1.4K
history.txt.gz 2008-06-09 13:50 785
multiz5way.sql 2008-06-09 13:50 1.4K
multiz5way.txt.gz 2008-06-09 13:50 4.3M
multiz5wayFrames.sql 2008-06-09 13:50 1.7K
multiz5wayFrames.txt.gz 2008-06-09 13:50 4.6M
multiz5waySummary.sql 2008-06-09 13:50 1.5K
multiz5waySummary.txt.gz 2008-06-09 13:50 1.1M
netGalGal3.sql 2008-06-09 13:50 2.2K
netGalGal3.txt.gz 2008-06-09 13:50 3.9M
netHg18.sql 2008-06-09 13:50 2.2K
netHg18.txt.gz 2008-06-09 13:51 4.0M
netMm9.sql 2008-06-09 13:51 2.2K
netMm9.txt.gz 2008-06-09 13:51 4.1M
netPetMar1.sql 2008-06-09 13:51 2.2K
netPetMar1.txt.gz 2008-06-09 13:51 3.4M
phastCons5way.sql 2008-06-09 13:51 1.7K
phastCons5way.txt.gz 2008-06-09 13:51 3.9M
phastConsElements5way.sql 2008-06-09 13:51 1.4K
phastConsElements5way.txt.gz 2008-06-09 13:51 1.3M
simpleRepeat.sql 2008-06-09 13:51 2.0K
simpleRepeat.txt.gz 2008-06-09 13:51 8.5M
windowmaskerSdust.sql 2008-06-09 13:51 1.4K
windowmaskerSdust.txt.gz 2008-06-09 13:52 39M
grp.sql 2014-03-02 03:40 1.4K
grp.txt.gz 2014-03-02 03:40 199
augustusGene.sql 2015-07-26 10:28 1.9K
augustusGene.txt.gz 2015-07-26 10:28 4.7M
all_est.sql 2016-12-18 06:00 2.1K
all_est.txt.gz 2016-12-18 06:00 20M
estOrientInfo.sql 2016-12-18 06:00 1.8K
estOrientInfo.txt.gz 2016-12-18 06:00 5.3M
intronEst.sql 2016-12-18 06:00 2.1K
intronEst.txt.gz 2016-12-18 06:00 7.1M
all_mrna.sql 2020-08-20 22:45 2.1K
all_mrna.txt.gz 2020-08-20 22:45 64K
xenoMrna.sql 2020-08-20 22:45 2.1K
xenoMrna.txt.gz 2020-08-20 22:45 263M
mrnaOrientInfo.sql 2020-08-20 23:00 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 23:00 138K
xenoRefGene.sql 2020-08-20 23:25 2.0K
xenoRefGene.txt.gz 2020-08-20 23:25 22M
xenoRefFlat.sql 2020-08-20 23:25 1.7K
xenoRefFlat.txt.gz 2020-08-20 23:25 19M
xenoRefSeqAli.sql 2020-08-20 23:25 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 23:25 22M
gbLoaded.sql 2020-08-20 23:25 1.6K
gbLoaded.txt.gz 2020-08-20 23:25 109K
trackDb.sql 2023-03-28 13:46 2.1K
trackDb.txt.gz 2023-03-28 13:46 39K
hgFindSpec.sql 2023-03-28 13:46 1.8K
hgFindSpec.txt.gz 2023-03-28 13:46 633
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 5.2K
tableList.sql 2024-11-24 03:14 1.6K
tableList.txt.gz 2024-11-24 03:14 3.2K
bigFiles.sql 2024-11-24 03:14 1.4K
bigFiles.txt.gz 2024-11-24 03:14 33