This directory contains a dump of the UCSC genome annotation database for the
    Sep. 2012 (JGI 7.0/xenTro7) assembly of the X. tropicalis genome
    (xenTro7, US DOE Joint Genome Institute (JGI-PGF)) 
from the X. tropicalis Genome Consortium.

The annotations were generated by UCSC and collaborators worldwide.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/80
    http://www.ncbi.nlm.nih.gov/assembly/515038
    http://www.ncbi.nlm.nih.gov/bioproject/12348

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=xenTro7
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/xenTro7/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/xenTro7/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/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 xenTro7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro7 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

1. The data may be freely downloaded, used in analyses, and repackaged
   in databases.

2. Users are free to use the data in scientific papers analyzing
   particular genes and regions if the provider of these data
   (DOE Joint Genome Institute) is properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. Any redistribution of the data should carry this notice.

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2015-12-21 10:02 63 ncbiRefSeqOther.txt.gz 2018-04-08 08:48 75 extNcbiRefSeq.txt.gz 2018-04-08 08:48 91 bigFiles.txt.gz 2022-08-14 03:10 94 grp.txt.gz 2015-12-21 10:02 206 history.txt.gz 2015-12-21 09:55 937 hgFindSpec.txt.gz 2022-03-29 14:46 1.1K gc5BaseBw.sql 2015-12-21 10:02 1.3K ncbiRefSeqOther.sql 2018-04-08 08:48 1.3K ncbiRefSeqCds.sql 2018-04-08 08:48 1.3K grp.sql 2015-12-21 10:02 1.3K ncbiRefSeqPepTable.sql 2018-04-08 08:48 1.4K bigFiles.sql 2022-08-14 03:10 1.4K chromInfo.sql 2015-12-21 10:02 1.4K chromAlias.sql 2018-02-18 09:00 1.4K ucscToINSDC.sql 2015-12-21 10:03 1.4K tableDescriptions.sql 2021-07-30 06:33 1.4K ucscToRefSeq.sql 2018-02-18 09:00 1.4K extNcbiRefSeq.sql 2018-04-08 08:48 1.4K microsat.sql 2015-12-21 10:02 1.5K windowmaskerSdust.sql 2015-12-21 10:03 1.5K cytoBandIdeo.sql 2015-12-21 10:02 1.5K chainRn6Link.sql 2017-03-28 10:44 1.5K chainHg38Link.sql 2015-12-21 09:57 1.5K chainMelGal5Link.sql 2017-03-21 07:23 1.5K chainNanPar1Link.sql 2019-02-24 03:22 1.5K seqNcbiRefSeq.sql 2018-04-08 08:48 1.5K tableList.sql 2022-08-14 03:10 1.6K history.sql 2015-12-21 09:55 1.6K gbLoaded.sql 2020-09-03 10:12 1.6K gap.sql 2015-12-21 10:02 1.6K gold.sql 2015-12-21 10:02 1.7K genscan.sql 2015-12-21 10:02 1.7K cpgIslandExt.sql 2015-12-21 10:02 1.7K chainRn6.sql 2017-03-28 10:31 1.7K chainHg38.sql 2015-12-21 09:56 1.7K refFlat.sql 2020-09-03 10:12 1.7K chainMelGal5.sql 2017-03-21 07:23 1.7K chainNanPar1.sql 2019-02-24 03:22 1.7K cpgIslandExtUnmasked.sql 2015-12-21 10:02 1.7K xenoRefFlat.sql 2020-09-03 10:12 1.7K hgFindSpec.sql 2022-03-29 14:46 1.8K estOrientInfo.sql 2015-12-21 10:02 1.8K mrnaOrientInfo.sql 2020-09-03 10:12 1.8K rmsk.sql 2015-12-21 10:02 1.9K refGene.sql 2020-09-03 10:12 1.9K mgcGenes.sql 2020-03-01 09:24 1.9K simpleRepeat.sql 2015-12-21 10:03 1.9K ncbiRefSeq.sql 2018-04-08 08:48 1.9K nestedRepeats.sql 2015-12-21 10:02 1.9K xenoRefGene.sql 2020-09-03 10:12 1.9K augustusGene.sql 2015-12-21 09:56 1.9K ncbiRefSeqCurated.sql 2018-04-08 08:48 2.0K ncbiRefSeqPredicted.sql 2018-04-08 08:48 2.0K ncbiRefSeqLink.sql 2018-04-08 08:48 2.0K trackDb.sql 2022-03-29 14:46 2.1K netRn6.sql 2017-03-28 12:02 2.1K netHg38.sql 2015-12-21 10:02 2.1K netMelGal5.sql 2017-03-21 07:24 2.1K netNanPar1.sql 2019-02-24 03:24 2.1K all_est.sql 2015-12-21 09:55 2.1K all_mrna.sql 2020-05-11 17:36 2.1K intronEst.sql 2015-12-21 09:56 2.1K refSeqAli.sql 2020-09-03 10:12 2.1K mgcFullMrna.sql 2020-03-01 09:24 2.1K ncbiRefSeqPsl.sql 2018-04-08 08:48 2.1K xenoRefSeqAli.sql 2020-09-03 10:12 2.1K tableList.txt.gz 2022-08-14 03:10 3.6K tableDescriptions.txt.gz 2021-07-30 06:33 6.3K cytoBandIdeo.txt.gz 2015-12-21 10:02 38K trackDb.txt.gz 2022-03-29 14:46 39K chromInfo.txt.gz 2015-12-21 10:02 43K gbLoaded.txt.gz 2020-09-03 10:12 46K ucscToINSDC.txt.gz 2015-12-21 10:03 56K ucscToRefSeq.txt.gz 2018-02-18 09:00 58K chromAlias.txt.gz 2018-02-18 09:00 66K microsat.txt.gz 2015-12-21 10:02 145K cpgIslandExt.txt.gz 2015-12-21 10:02 261K ncbiRefSeqCds.txt.gz 2018-04-08 08:48 277K mrnaOrientInfo.txt.gz 2020-09-03 10:12 521K gap.txt.gz 2015-12-21 10:02 633K seqNcbiRefSeq.txt.gz 2018-04-08 08:48 667K mgcGenes.txt.gz 2020-03-01 09:24 781K refFlat.txt.gz 2020-09-03 10:12 855K cpgIslandExtUnmasked.txt.gz 2015-12-21 10:02 867K ncbiRefSeqCurated.txt.gz 2018-04-08 08:48 872K mgcFullMrna.txt.gz 2020-03-01 09:24 904K refGene.txt.gz 2020-09-03 10:12 913K gold.txt.gz 2015-12-21 10:02 921K refSeqAli.txt.gz 2020-09-03 10:12 954K ncbiRefSeqLink.txt.gz 2018-04-08 08:48 1.4M all_mrna.txt.gz 2020-05-11 17:36 1.9M augustusGene.txt.gz 2015-12-21 09:56 2.2M ncbiRefSeqPredicted.txt.gz 2018-04-08 08:48 2.3M genscan.txt.gz 2015-12-21 10:02 2.3M ncbiRefSeq.txt.gz 2018-04-08 08:48 2.9M ncbiRefSeqPsl.txt.gz 2018-04-08 08:48 3.6M nestedRepeats.txt.gz 2015-12-21 10:02 4.4M netMelGal5.txt.gz 2017-03-21 07:24 5.5M chainMelGal5.txt.gz 2017-03-21 07:23 6.6M ncbiRefSeqPepTable.txt.gz 2018-04-08 08:48 9.6M netHg38.txt.gz 2015-12-21 10:02 11M netRn6.txt.gz 2017-03-28 12:02 12M netNanPar1.txt.gz 2019-02-24 03:24 12M estOrientInfo.txt.gz 2015-12-21 10:02 14M simpleRepeat.txt.gz 2015-12-21 10:03 19M xenoRefSeqAli.txt.gz 2020-09-03 10:12 21M xenoRefFlat.txt.gz 2020-09-03 10:12 22M chainMelGal5Link.txt.gz 2017-03-21 07:23 22M xenoRefGene.txt.gz 2020-09-03 10:12 24M intronEst.txt.gz 2015-12-21 09:56 33M all_est.txt.gz 2015-12-21 09:55 52M rmsk.txt.gz 2015-12-21 10:03 57M windowmaskerSdust.txt.gz 2015-12-21 10:03 64M chainNanPar1.txt.gz 2019-02-24 03:22 94M chainHg38.txt.gz 2015-12-21 09:56 229M chainNanPar1Link.txt.gz 2019-02-24 03:23 283M chainRn6.txt.gz 2017-03-28 10:34 318M chainHg38Link.txt.gz 2015-12-21 09:58 1.0G chainRn6Link.txt.gz 2017-03-28 11:06 1.4G