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 -
bigFiles.txt.gz 2024-11-24 03:14 33
bigFiles.sql 2024-11-24 03:14 1.4K
tableList.txt.gz 2024-11-24 03:14 3.2K
tableList.sql 2024-11-24 03:14 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 5.2K
tableDescriptions.sql 2024-11-23 02:03 1.5K
hgFindSpec.txt.gz 2023-03-28 13:46 633
hgFindSpec.sql 2023-03-28 13:46 1.8K
trackDb.txt.gz 2023-03-28 13:46 39K
trackDb.sql 2023-03-28 13:46 2.1K
gbLoaded.txt.gz 2020-08-20 23:25 109K
gbLoaded.sql 2020-08-20 23:25 1.6K
xenoRefSeqAli.txt.gz 2020-08-20 23:25 22M
xenoRefSeqAli.sql 2020-08-20 23:25 2.1K
xenoRefFlat.txt.gz 2020-08-20 23:25 19M
xenoRefFlat.sql 2020-08-20 23:25 1.7K
xenoRefGene.txt.gz 2020-08-20 23:25 22M
xenoRefGene.sql 2020-08-20 23:25 2.0K
mrnaOrientInfo.txt.gz 2020-08-20 23:00 138K
mrnaOrientInfo.sql 2020-08-20 23:00 1.8K
xenoMrna.txt.gz 2020-08-20 22:45 263M
xenoMrna.sql 2020-08-20 22:45 2.1K
all_mrna.txt.gz 2020-08-20 22:45 64K
all_mrna.sql 2020-08-20 22:45 2.1K
intronEst.txt.gz 2016-12-18 06:00 7.1M
intronEst.sql 2016-12-18 06:00 2.1K
estOrientInfo.txt.gz 2016-12-18 06:00 5.3M
estOrientInfo.sql 2016-12-18 06:00 1.8K
all_est.txt.gz 2016-12-18 06:00 20M
all_est.sql 2016-12-18 06:00 2.1K
augustusGene.txt.gz 2015-07-26 10:28 4.7M
augustusGene.sql 2015-07-26 10:28 1.9K
grp.txt.gz 2014-03-02 03:40 199
grp.sql 2014-03-02 03:40 1.4K
windowmaskerSdust.txt.gz 2008-06-09 13:52 39M
windowmaskerSdust.sql 2008-06-09 13:51 1.4K
simpleRepeat.txt.gz 2008-06-09 13:51 8.5M
simpleRepeat.sql 2008-06-09 13:51 2.0K
phastConsElements5way.txt.gz 2008-06-09 13:51 1.3M
phastConsElements5way.sql 2008-06-09 13:51 1.4K
phastCons5way.txt.gz 2008-06-09 13:51 3.9M
phastCons5way.sql 2008-06-09 13:51 1.7K
netPetMar1.txt.gz 2008-06-09 13:51 3.4M
netPetMar1.sql 2008-06-09 13:51 2.2K
netMm9.txt.gz 2008-06-09 13:51 4.1M
netMm9.sql 2008-06-09 13:51 2.2K
netHg18.txt.gz 2008-06-09 13:51 4.0M
netHg18.sql 2008-06-09 13:50 2.2K
netGalGal3.txt.gz 2008-06-09 13:50 3.9M
netGalGal3.sql 2008-06-09 13:50 2.2K
multiz5waySummary.txt.gz 2008-06-09 13:50 1.1M
multiz5waySummary.sql 2008-06-09 13:50 1.5K
multiz5wayFrames.txt.gz 2008-06-09 13:50 4.6M
multiz5wayFrames.sql 2008-06-09 13:50 1.7K
multiz5way.txt.gz 2008-06-09 13:50 4.3M
multiz5way.sql 2008-06-09 13:50 1.4K
history.txt.gz 2008-06-09 13:50 785
history.sql 2008-06-09 13:50 1.4K
gc5Base.txt.gz 2008-06-09 13:50 3.8M
gc5Base.sql 2008-06-09 13:50 1.7K
extFile.txt.gz 2008-06-09 13:47 133
extFile.sql 2008-06-09 13:47 1.3K
chromInfo.txt.gz 2008-06-09 13:47 82
chromInfo.sql 2008-06-09 13:47 1.2K
chrUn_gold.txt.gz 2008-06-09 13:47 57K
chrUn_gold.sql 2008-06-09 13:47 1.6K
chrUn_gap.txt.gz 2008-06-09 13:47 1.2M
chrUn_gap.sql 2008-06-09 13:47 1.5K
chrUn_chainPetMar1Link.txt.gz 2008-06-09 13:47 44M
chrUn_chainPetMar1Link.sql 2008-06-09 13:46 1.4K
chrUn_chainPetMar1.txt.gz 2008-06-09 13:46 9.7M
chrUn_chainPetMar1.sql 2008-06-09 13:46 1.7K
chrUn_chainMm9Link.txt.gz 2008-06-09 13:46 23M
chrUn_chainMm9Link.sql 2008-06-09 13:45 1.4K
chrUn_chainMm9.txt.gz 2008-06-09 13:45 4.9M
chrUn_chainMm9.sql 2008-06-09 13:45 1.7K
chrUn_chainHg18Link.txt.gz 2008-06-09 13:45 29M
chrUn_chainHg18Link.sql 2008-06-09 13:45 1.4K
chrUn_chainHg18.txt.gz 2008-06-09 13:44 6.4M
chrUn_chainHg18.sql 2008-06-09 13:44 1.7K
chrUn_chainGalGal3Link.txt.gz 2008-06-09 13:44 15M
chrUn_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrUn_chainGalGal3.txt.gz 2008-06-09 13:44 2.6M
chrUn_chainGalGal3.sql 2008-06-09 13:44 1.7K
chrM_gold.txt.gz 2008-06-09 13:44 68
chrM_gold.sql 2008-06-09 13:44 1.6K
chrM_gap.txt.gz 2008-06-09 13:44 33
chrM_gap.sql 2008-06-09 13:44 1.5K
chrM_chainPetMar1Link.txt.gz 2008-06-09 13:44 4.8K
chrM_chainPetMar1Link.sql 2008-06-09 13:44 1.4K
chrM_chainPetMar1.txt.gz 2008-06-09 13:44 882
chrM_chainPetMar1.sql 2008-06-09 13:44 1.7K
chrM_chainMm9Link.txt.gz 2008-06-09 13:44 7.2K
chrM_chainMm9Link.sql 2008-06-09 13:44 1.4K
chrM_chainMm9.txt.gz 2008-06-09 13:44 1.0K
chrM_chainMm9.sql 2008-06-09 13:44 1.6K
chrM_chainHg18Link.txt.gz 2008-06-09 13:44 71K
chrM_chainHg18Link.sql 2008-06-09 13:44 1.4K
chrM_chainHg18.txt.gz 2008-06-09 13:44 6.0K
chrM_chainHg18.sql 2008-06-09 13:44 1.7K
chrM_chainGalGal3Link.txt.gz 2008-06-09 13:44 2.1K
chrM_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrM_chainGalGal3.txt.gz 2008-06-09 13:44 256
chrM_chainGalGal3.sql 2008-06-09 13:44 1.7K
blastHg18KG.txt.gz 2008-06-09 13:44 2.2M
blastHg18KG.sql 2008-06-09 13:44 2.1K