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