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 - all_est.sql 2016-12-18 06:00 2.1K all_est.txt.gz 2016-12-18 06:00 20M all_mrna.sql 2020-08-20 22:45 2.1K all_mrna.txt.gz 2020-08-20 22:45 64K augustusGene.sql 2015-07-26 10:28 1.9K augustusGene.txt.gz 2015-07-26 10:28 4.7M bigFiles.sql 2021-05-09 03:05 1.4K bigFiles.txt.gz 2021-05-09 03:05 33 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 estOrientInfo.sql 2016-12-18 06:00 1.8K estOrientInfo.txt.gz 2016-12-18 06:00 5.3M extFile.sql 2008-06-09 13:47 1.3K extFile.txt.gz 2008-06-09 13:47 133 gbLoaded.sql 2020-08-20 23:25 1.6K gbLoaded.txt.gz 2020-08-20 23:25 109K gc5Base.sql 2008-06-09 13:50 1.7K gc5Base.txt.gz 2008-06-09 13:50 3.8M grp.sql 2014-03-02 03:40 1.4K grp.txt.gz 2014-03-02 03:40 199 hgFindSpec.sql 2020-12-06 07:41 1.7K hgFindSpec.txt.gz 2020-12-06 07:41 586 history.sql 2008-06-09 13:50 1.4K history.txt.gz 2008-06-09 13:50 785 intronEst.sql 2016-12-18 06:00 2.1K intronEst.txt.gz 2016-12-18 06:00 7.1M mrnaOrientInfo.sql 2020-08-20 23:00 1.8K mrnaOrientInfo.txt.gz 2020-08-20 23:00 138K 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 tableDescriptions.sql 2019-07-21 03:41 1.4K tableDescriptions.txt.gz 2019-07-21 03:41 5.1K tableList.sql 2021-05-09 03:05 1.6K tableList.txt.gz 2021-05-09 03:05 3.1K trackDb.sql 2020-12-06 07:41 2.0K trackDb.txt.gz 2020-12-06 07:41 37K windowmaskerSdust.sql 2008-06-09 13:51 1.4K windowmaskerSdust.txt.gz 2008-06-09 13:52 39M xenoMrna.sql 2020-08-20 22:45 2.1K xenoMrna.txt.gz 2020-08-20 22:45 263M xenoRefFlat.sql 2020-08-20 23:25 1.7K xenoRefFlat.txt.gz 2020-08-20 23:25 19M xenoRefGene.sql 2020-08-20 23:25 1.9K xenoRefGene.txt.gz 2020-08-20 23:25 22M xenoRefSeqAli.sql 2020-08-20 23:25 2.1K xenoRefSeqAli.txt.gz 2020-08-20 23:25 22M