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 2024-03-24 03:21 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_pushedout.txt.gz 2021-12-27 12:22 596 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 bigFiles.sql 2024-03-24 03:21 1.4K grp.sql 2014-03-02 03:40 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 tableDescriptions.sql 2024-03-23 02:03 1.4K phastConsElements5way.sql 2008-06-09 13:51 1.4K 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 tableList.sql 2024-03-24 03:21 1.6K chrM_gold.sql 2008-06-09 13:44 1.6K chrUn_gold.sql 2008-06-09 13:47 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 hgFindSpec_pushedout.sql 2021-12-27 12:22 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 trackDb_pushedout.sql 2021-12-27 12:22 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 2024-03-24 03:21 3.3K chrM_chainPetMar1Link.txt.gz 2008-06-09 13:44 4.8K tableDescriptions.txt.gz 2024-03-23 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_pushedout.txt.gz 2021-12-27 12:22 37K 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