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 2024-12-08 03:16 33
chrM_gap.txt.gz 2008-06-09 13:44 33
chrM_gold.txt.gz 2008-06-09 13:44 68
chromInfo.txt.gz 2008-06-09 13:47 82
extFile.txt.gz 2008-06-09 13:47 133
grp.txt.gz 2014-03-02 03:40 199
chrM_chainGalGal3.txt.gz 2008-06-09 13:44 256
hgFindSpec.txt.gz 2023-03-28 13:46 633
history.txt.gz 2008-06-09 13:50 785
chrM_chainPetMar1.txt.gz 2008-06-09 13:44 882
chrM_chainMm9.txt.gz 2008-06-09 13:44 1.0K
chromInfo.sql 2008-06-09 13:47 1.2K
extFile.sql 2008-06-09 13:47 1.3K
windowmaskerSdust.sql 2008-06-09 13:51 1.4K
grp.sql 2014-03-02 03:40 1.4K
bigFiles.sql 2024-12-08 03:16 1.4K
chrM_chainMm9Link.sql 2008-06-09 13:44 1.4K
chrM_chainHg18Link.sql 2008-06-09 13:44 1.4K
chrUn_chainMm9Link.sql 2008-06-09 13:45 1.4K
multiz5way.sql 2008-06-09 13:50 1.4K
chrUn_chainHg18Link.sql 2008-06-09 13:45 1.4K
chrM_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrM_chainPetMar1Link.sql 2008-06-09 13:44 1.4K
chrUn_chainGalGal3Link.sql 2008-06-09 13:44 1.4K
chrUn_chainPetMar1Link.sql 2008-06-09 13:46 1.4K
history.sql 2008-06-09 13:50 1.4K
phastConsElements5way.sql 2008-06-09 13:51 1.4K
tableDescriptions.sql 2024-12-07 02:03 1.5K
multiz5waySummary.sql 2008-06-09 13:50 1.5K
chrM_gap.sql 2008-06-09 13:44 1.5K
chrUn_gap.sql 2008-06-09 13:47 1.5K
chrM_gold.sql 2008-06-09 13:44 1.6K
chrUn_gold.sql 2008-06-09 13:47 1.6K
tableList.sql 2024-12-08 03:16 1.6K
gbLoaded.sql 2020-08-20 23:25 1.6K
chrM_chainMm9.sql 2008-06-09 13:44 1.6K
chrM_chainHg18.sql 2008-06-09 13:44 1.7K
chrUn_chainMm9.sql 2008-06-09 13:45 1.7K
chrUn_chainHg18.sql 2008-06-09 13:44 1.7K
chrM_chainGalGal3.sql 2008-06-09 13:44 1.7K
chrM_chainPetMar1.sql 2008-06-09 13:44 1.7K
chrUn_chainGalGal3.sql 2008-06-09 13:44 1.7K
chrUn_chainPetMar1.sql 2008-06-09 13:46 1.7K
multiz5wayFrames.sql 2008-06-09 13:50 1.7K
gc5Base.sql 2008-06-09 13:50 1.7K
phastCons5way.sql 2008-06-09 13:51 1.7K
xenoRefFlat.sql 2020-08-20 23:25 1.7K
hgFindSpec.sql 2023-03-28 13:46 1.8K
estOrientInfo.sql 2016-12-18 06:00 1.8K
mrnaOrientInfo.sql 2020-08-20 23:00 1.8K
augustusGene.sql 2015-07-26 10:28 1.9K
xenoRefGene.sql 2020-08-20 23:25 2.0K
simpleRepeat.sql 2008-06-09 13:51 2.0K
trackDb.sql 2023-03-28 13:46 2.1K
chrM_chainGalGal3Link.txt.gz 2008-06-09 13:44 2.1K
all_est.sql 2016-12-18 06:00 2.1K
intronEst.sql 2016-12-18 06:00 2.1K
all_mrna.sql 2020-08-20 22:45 2.1K
xenoMrna.sql 2020-08-20 22:45 2.1K
blastHg18KG.sql 2008-06-09 13:44 2.1K
xenoRefSeqAli.sql 2020-08-20 23:25 2.1K
netMm9.sql 2008-06-09 13:51 2.2K
netHg18.sql 2008-06-09 13:50 2.2K
netGalGal3.sql 2008-06-09 13:50 2.2K
netPetMar1.sql 2008-06-09 13:51 2.2K
tableList.txt.gz 2024-12-08 03:16 3.2K
chrM_chainPetMar1Link.txt.gz 2008-06-09 13:44 4.8K
tableDescriptions.txt.gz 2024-12-07 02:03 5.2K
chrM_chainHg18.txt.gz 2008-06-09 13:44 6.0K
chrM_chainMm9Link.txt.gz 2008-06-09 13:44 7.2K
trackDb.txt.gz 2023-03-28 13:46 39K
chrUn_gold.txt.gz 2008-06-09 13:47 57K
all_mrna.txt.gz 2020-08-20 22:45 64K
chrM_chainHg18Link.txt.gz 2008-06-09 13:44 71K
gbLoaded.txt.gz 2020-08-20 23:25 109K
mrnaOrientInfo.txt.gz 2020-08-20 23:00 138K
multiz5waySummary.txt.gz 2008-06-09 13:50 1.1M
chrUn_gap.txt.gz 2008-06-09 13:47 1.2M
phastConsElements5way.txt.gz 2008-06-09 13:51 1.3M
blastHg18KG.txt.gz 2008-06-09 13:44 2.2M
chrUn_chainGalGal3.txt.gz 2008-06-09 13:44 2.6M
netPetMar1.txt.gz 2008-06-09 13:51 3.4M
gc5Base.txt.gz 2008-06-09 13:50 3.8M
netGalGal3.txt.gz 2008-06-09 13:50 3.9M
phastCons5way.txt.gz 2008-06-09 13:51 3.9M
netHg18.txt.gz 2008-06-09 13:51 4.0M
netMm9.txt.gz 2008-06-09 13:51 4.1M
multiz5way.txt.gz 2008-06-09 13:50 4.3M
multiz5wayFrames.txt.gz 2008-06-09 13:50 4.6M
augustusGene.txt.gz 2015-07-26 10:28 4.7M
chrUn_chainMm9.txt.gz 2008-06-09 13:45 4.9M
estOrientInfo.txt.gz 2016-12-18 06:00 5.3M
chrUn_chainHg18.txt.gz 2008-06-09 13:44 6.4M
intronEst.txt.gz 2016-12-18 06:00 7.1M
simpleRepeat.txt.gz 2008-06-09 13:51 8.5M
chrUn_chainPetMar1.txt.gz 2008-06-09 13:46 9.7M
chrUn_chainGalGal3Link.txt.gz 2008-06-09 13:44 15M
xenoRefFlat.txt.gz 2020-08-20 23:25 19M
all_est.txt.gz 2016-12-18 06:00 20M
xenoRefSeqAli.txt.gz 2020-08-20 23:25 22M
xenoRefGene.txt.gz 2020-08-20 23:25 22M
chrUn_chainMm9Link.txt.gz 2008-06-09 13:46 23M
chrUn_chainHg18Link.txt.gz 2008-06-09 13:45 29M
windowmaskerSdust.txt.gz 2008-06-09 13:52 39M
chrUn_chainPetMar1Link.txt.gz 2008-06-09 13:47 44M
xenoMrna.txt.gz 2020-08-20 22:45 263M