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 - xenoRefSeqAli.txt.gz 2020-09-03 10:12 21M xenoRefSeqAli.sql 2020-09-03 10:12 2.1K xenoRefGene.txt.gz 2020-09-03 10:12 24M xenoRefGene.sql 2020-09-03 10:12 1.9K xenoRefFlat.txt.gz 2020-09-03 10:12 22M xenoRefFlat.sql 2020-09-03 10:12 1.7K windowmaskerSdust.txt.gz 2015-12-21 10:03 64M windowmaskerSdust.sql 2015-12-21 10:03 1.5K ucscToRefSeq.txt.gz 2018-02-18 09:00 58K ucscToRefSeq.sql 2018-02-18 09:00 1.4K ucscToINSDC.txt.gz 2015-12-21 10:03 56K ucscToINSDC.sql 2015-12-21 10:03 1.4K trackDb.txt.gz 2022-03-29 14:46 39K trackDb.sql 2022-03-29 14:46 2.1K tableList.txt.gz 2022-11-27 03:10 3.6K tableList.sql 2022-11-27 03:10 1.6K tableDescriptions.txt.gz 2021-07-30 06:33 6.3K tableDescriptions.sql 2021-07-30 06:33 1.4K simpleRepeat.txt.gz 2015-12-21 10:03 19M simpleRepeat.sql 2015-12-21 10:03 1.9K seqNcbiRefSeq.txt.gz 2018-04-08 08:48 667K seqNcbiRefSeq.sql 2018-04-08 08:48 1.5K rmsk.txt.gz 2015-12-21 10:03 57M rmsk.sql 2015-12-21 10:02 1.9K refSeqAli.txt.gz 2020-09-03 10:12 954K refSeqAli.sql 2020-09-03 10:12 2.1K refGene.txt.gz 2020-09-03 10:12 913K refGene.sql 2020-09-03 10:12 1.9K refFlat.txt.gz 2020-09-03 10:12 855K refFlat.sql 2020-09-03 10:12 1.7K netRn6.txt.gz 2017-03-28 12:02 12M netRn6.sql 2017-03-28 12:02 2.1K netNanPar1.txt.gz 2019-02-24 03:24 12M netNanPar1.sql 2019-02-24 03:24 2.1K netMelGal5.txt.gz 2017-03-21 07:24 5.5M netMelGal5.sql 2017-03-21 07:24 2.1K netHg38.txt.gz 2015-12-21 10:02 11M netHg38.sql 2015-12-21 10:02 2.1K nestedRepeats.txt.gz 2015-12-21 10:02 4.4M nestedRepeats.sql 2015-12-21 10:02 1.9K ncbiRefSeqPsl.txt.gz 2018-04-08 08:48 3.6M ncbiRefSeqPsl.sql 2018-04-08 08:48 2.1K ncbiRefSeqPredicted.txt.gz 2018-04-08 08:48 2.3M ncbiRefSeqPredicted.sql 2018-04-08 08:48 2.0K ncbiRefSeqPepTable.txt.gz 2018-04-08 08:48 9.6M ncbiRefSeqPepTable.sql 2018-04-08 08:48 1.4K ncbiRefSeqOther.txt.gz 2018-04-08 08:48 75 ncbiRefSeqOther.sql 2018-04-08 08:48 1.3K ncbiRefSeqLink.txt.gz 2018-04-08 08:48 1.4M ncbiRefSeqLink.sql 2018-04-08 08:48 2.0K ncbiRefSeqCurated.txt.gz 2018-04-08 08:48 872K ncbiRefSeqCurated.sql 2018-04-08 08:48 2.0K ncbiRefSeqCds.txt.gz 2018-04-08 08:48 277K ncbiRefSeqCds.sql 2018-04-08 08:48 1.3K ncbiRefSeq.txt.gz 2018-04-08 08:48 2.9M ncbiRefSeq.sql 2018-04-08 08:48 1.9K mrnaOrientInfo.txt.gz 2020-09-03 10:12 521K mrnaOrientInfo.sql 2020-09-03 10:12 1.8K microsat.txt.gz 2015-12-21 10:02 145K microsat.sql 2015-12-21 10:02 1.5K mgcGenes.txt.gz 2020-03-01 09:24 781K mgcGenes.sql 2020-03-01 09:24 1.9K mgcFullMrna.txt.gz 2020-03-01 09:24 904K mgcFullMrna.sql 2020-03-01 09:24 2.1K intronEst.txt.gz 2015-12-21 09:56 33M intronEst.sql 2015-12-21 09:56 2.1K history.txt.gz 2015-12-21 09:55 937 history.sql 2015-12-21 09:55 1.6K hgFindSpec.txt.gz 2022-03-29 14:46 1.1K hgFindSpec.sql 2022-03-29 14:46 1.8K grp.txt.gz 2015-12-21 10:02 206 grp.sql 2015-12-21 10:02 1.3K gold.txt.gz 2015-12-21 10:02 921K gold.sql 2015-12-21 10:02 1.7K genscan.txt.gz 2015-12-21 10:02 2.3M genscan.sql 2015-12-21 10:02 1.7K gc5BaseBw.txt.gz 2015-12-21 10:02 63 gc5BaseBw.sql 2015-12-21 10:02 1.3K gbLoaded.txt.gz 2020-09-03 10:12 46K gbLoaded.sql 2020-09-03 10:12 1.6K gap.txt.gz 2015-12-21 10:02 633K gap.sql 2015-12-21 10:02 1.6K extNcbiRefSeq.txt.gz 2018-04-08 08:48 91 extNcbiRefSeq.sql 2018-04-08 08:48 1.4K estOrientInfo.txt.gz 2015-12-21 10:02 14M estOrientInfo.sql 2015-12-21 10:02 1.8K cytoBandIdeo.txt.gz 2015-12-21 10:02 38K cytoBandIdeo.sql 2015-12-21 10:02 1.5K cpgIslandExtUnmasked.txt.gz 2015-12-21 10:02 867K cpgIslandExtUnmasked.sql 2015-12-21 10:02 1.7K cpgIslandExt.txt.gz 2015-12-21 10:02 261K cpgIslandExt.sql 2015-12-21 10:02 1.7K chromInfo.txt.gz 2015-12-21 10:02 43K chromInfo.sql 2015-12-21 10:02 1.4K chromAlias.txt.gz 2018-02-18 09:00 66K chromAlias.sql 2018-02-18 09:00 1.4K chainRn6Link.txt.gz 2017-03-28 11:06 1.4G chainRn6Link.sql 2017-03-28 10:44 1.5K chainRn6.txt.gz 2017-03-28 10:34 318M chainRn6.sql 2017-03-28 10:31 1.7K chainNanPar1Link.txt.gz 2019-02-24 03:23 283M chainNanPar1Link.sql 2019-02-24 03:22 1.5K chainNanPar1.txt.gz 2019-02-24 03:22 94M chainNanPar1.sql 2019-02-24 03:22 1.7K chainMelGal5Link.txt.gz 2017-03-21 07:23 22M chainMelGal5Link.sql 2017-03-21 07:23 1.5K chainMelGal5.txt.gz 2017-03-21 07:23 6.6M chainMelGal5.sql 2017-03-21 07:23 1.7K chainHg38Link.txt.gz 2015-12-21 09:58 1.0G chainHg38Link.sql 2015-12-21 09:57 1.5K chainHg38.txt.gz 2015-12-21 09:56 229M chainHg38.sql 2015-12-21 09:56 1.7K bigFiles.txt.gz 2022-11-27 03:10 94 bigFiles.sql 2022-11-27 03:10 1.4K augustusGene.txt.gz 2015-12-21 09:56 2.2M augustusGene.sql 2015-12-21 09:56 1.9K all_mrna.txt.gz 2020-05-11 17:36 1.9M all_mrna.sql 2020-05-11 17:36 2.1K all_est.txt.gz 2015-12-21 09:55 52M all_est.sql 2015-12-21 09:55 2.1K