This directory contains a dump of the UCSC genome annotation database for the
    Nov. 2019 (UCB_Xtro_10.0/xenTro10) assembly of the X. tropicalis genome
    (xenTro10, University of California, Berkeley) 
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:
    https://www.ncbi.nlm.nih.gov/genome/80
    https://www.ncbi.nlm.nih.gov/genome/assembly/5323661
    https://www.ncbi.nlm.nih.gov/bioproject/577946
    https://www.ncbi.nlm.nih.gov/biosample/SAMN13041969

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=xenTro10
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.soe.ucsc.edu, then go to
the directory goldenPath/xenTro10/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.soe.ucsc.edu/goldenPath/xenTro10/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

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 xenTro10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro10 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

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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 2021-02-22 12:16 67 crisprAllTargets.txt.gz 2021-02-25 03:01 70 ncbiRefSeqOther.txt.gz 2021-02-22 22:04 76 extNcbiRefSeq.txt.gz 2021-02-22 22:04 92 bigFiles.txt.gz 2022-08-14 03:03 120 grp.txt.gz 2021-02-22 12:16 213 history.txt.gz 2021-03-31 14:18 1.0K cytoBandIdeo.txt.gz 2021-02-22 12:39 1.0K hgFindSpec.txt.gz 2021-07-16 05:18 1.0K chromInfo.txt.gz 2021-02-22 12:16 1.1K gc5BaseBw.sql 2021-02-22 12:16 1.3K ncbiRefSeqOther.sql 2021-02-22 22:04 1.3K crisprAllTargets.sql 2021-02-25 03:01 1.3K gbLoaded.txt.gz 2021-03-25 15:56 1.3K ncbiRefSeqCds.sql 2021-02-22 22:04 1.4K grp.sql 2021-02-22 12:16 1.4K bigFiles.sql 2022-08-14 03:03 1.4K ncbiRefSeqPepTable.sql 2021-03-31 14:18 1.4K chromInfo.sql 2021-02-22 12:16 1.4K ucscToRefSeq.txt.gz 2021-02-22 13:28 1.4K ucscToINSDC.txt.gz 2021-02-22 13:28 1.4K tableDescriptions.sql 2021-07-15 06:36 1.4K chromAlias.sql 2021-02-22 13:19 1.4K ucscToINSDC.sql 2021-02-22 13:28 1.4K ucscToRefSeq.sql 2021-02-22 13:28 1.5K extNcbiRefSeq.sql 2021-02-22 22:04 1.5K microsat.sql 2021-02-22 16:05 1.5K windowmaskerSdust.sql 2021-02-22 16:52 1.5K cytoBandIdeo.sql 2021-02-22 12:39 1.5K chainHg38Link.sql 2021-02-23 12:30 1.6K chainMm10Link.sql 2021-02-23 07:59 1.6K chainMm39Link.sql 2021-02-23 07:47 1.6K tableList.sql 2022-08-14 03:03 1.6K seqNcbiRefSeq.sql 2021-02-22 22:04 1.6K history.sql 2021-03-31 14:18 1.6K gbLoaded.sql 2021-03-25 15:56 1.6K gap.sql 2021-02-22 12:15 1.6K gold.sql 2021-02-22 12:15 1.7K genscan.sql 2021-02-23 11:30 1.7K cpgIslandExt.sql 2021-02-22 21:35 1.7K chainHg38.sql 2021-02-23 12:03 1.7K chainMm10.sql 2021-02-23 07:54 1.7K chainMm39.sql 2021-02-23 07:45 1.7K refFlat.sql 2021-03-24 15:45 1.7K cpgIslandExtUnmasked.sql 2021-02-22 12:36 1.7K xenoRefFlat.sql 2021-03-24 15:45 1.7K hgFindSpec.sql 2021-07-16 05:18 1.8K estOrientInfo.sql 2021-03-25 15:56 1.8K mrnaOrientInfo.sql 2021-03-25 15:56 1.8K rmsk.sql 2021-02-22 18:31 1.9K refGene.sql 2021-03-24 15:45 1.9K simpleRepeat.sql 2021-02-22 14:42 1.9K ncbiRefSeq.sql 2021-02-22 21:40 2.0K nestedRepeats.sql 2021-02-22 18:32 2.0K xenoRefGene.sql 2021-03-24 15:45 2.0K augustusGene.sql 2021-02-22 22:24 2.0K ncbiRefSeqCurated.sql 2021-02-22 21:40 2.0K ncbiRefSeqPredicted.sql 2021-02-22 21:40 2.0K ncbiRefSeqLink.sql 2021-03-31 11:37 2.0K trackDb.sql 2021-07-16 05:18 2.1K netHg38.sql 2021-02-23 12:32 2.1K netMm10.sql 2021-02-23 08:00 2.1K netMm39.sql 2021-02-23 07:49 2.1K all_est.sql 2021-03-25 15:56 2.1K all_mrna.sql 2021-03-24 15:19 2.1K intronEst.sql 2021-03-25 15:56 2.1K refSeqAli.sql 2021-03-24 15:45 2.1K ncbiRefSeqPsl.sql 2021-02-22 21:40 2.1K xenoRefSeqAli.sql 2021-03-24 15:45 2.1K chromAlias.txt.gz 2021-02-22 13:19 2.6K tableList.txt.gz 2022-08-14 03:03 3.2K tableDescriptions.txt.gz 2021-07-15 06:36 6.1K gap.txt.gz 2021-02-22 12:15 10K gold.txt.gz 2021-02-22 12:15 16K trackDb.txt.gz 2021-07-16 05:18 35K microsat.txt.gz 2021-02-22 16:05 156K ncbiRefSeqCds.txt.gz 2021-02-22 22:04 313K cpgIslandExt.txt.gz 2021-02-22 21:35 342K mrnaOrientInfo.txt.gz 2021-03-25 15:56 510K seqNcbiRefSeq.txt.gz 2021-02-22 22:04 759K refFlat.txt.gz 2021-03-24 15:45 848K ncbiRefSeqCurated.txt.gz 2021-02-22 21:40 924K refGene.txt.gz 2021-03-24 15:45 928K refSeqAli.txt.gz 2021-03-24 15:45 961K cpgIslandExtUnmasked.txt.gz 2021-02-22 12:36 1.1M ncbiRefSeqLink.txt.gz 2021-03-31 11:37 1.8M all_mrna.txt.gz 2021-03-24 15:19 1.8M augustusGene.txt.gz 2021-02-22 22:24 2.3M genscan.txt.gz 2021-02-23 11:30 2.4M ncbiRefSeqPredicted.txt.gz 2021-02-22 21:40 2.6M ncbiRefSeq.txt.gz 2021-02-22 21:40 3.2M ncbiRefSeqPsl.txt.gz 2021-02-22 21:40 4.1M nestedRepeats.txt.gz 2021-02-22 18:32 5.1M xenoRefFlat.txt.gz 2021-03-24 15:45 6.0M xenoRefGene.txt.gz 2021-03-24 15:45 6.7M netMm39.txt.gz 2021-02-23 07:49 8.2M ncbiRefSeqPepTable.txt.gz 2021-03-31 14:18 11M xenoRefSeqAli.txt.gz 2021-03-24 15:45 11M netMm10.txt.gz 2021-02-23 08:00 12M estOrientInfo.txt.gz 2021-03-25 15:56 15M netHg38.txt.gz 2021-02-23 12:32 15M simpleRepeat.txt.gz 2021-02-22 14:42 22M intronEst.txt.gz 2021-03-25 15:56 33M all_est.txt.gz 2021-03-25 15:56 53M chainMm39.txt.gz 2021-02-23 07:45 59M rmsk.txt.gz 2021-02-22 18:31 61M windowmaskerSdust.txt.gz 2021-02-22 16:52 62M chainMm10.txt.gz 2021-02-23 07:54 111M chainMm39Link.txt.gz 2021-02-23 07:47 270M chainHg38.txt.gz 2021-02-23 12:03 435M chainMm10Link.txt.gz 2021-02-23 07:59 619M chainHg38Link.txt.gz 2021-02-23 12:30 2.4G