This directory contains a dump of the UCSC genome annotation database for the
    Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) assembly of the X. tropicalis genome
    (xenTro9, DOE Joint Genome Institute) 
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/genome/assembly/768701
    http://www.ncbi.nlm.nih.gov/bioproject/205740

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=xenTro9
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/xenTro9/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/xenTro9/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/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 xenTro9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro9 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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 - all_est.sql 2017-12-05 11:32 2.1K all_est.txt.gz 2017-12-05 11:32 51M all_mrna.sql 2020-08-20 18:44 2.1K all_mrna.txt.gz 2020-08-20 18:44 1.8M augustusGene.sql 2017-12-05 11:33 1.9K augustusGene.txt.gz 2017-12-05 11:33 2.2M bigFiles.sql 2021-05-02 03:04 1.4K bigFiles.txt.gz 2021-05-02 03:04 95 chainAnoCar2.sql 2017-12-05 11:37 1.7K chainAnoCar2.txt.gz 2017-12-05 11:37 45M chainAnoCar2Link.sql 2017-12-05 11:38 1.5K chainAnoCar2Link.txt.gz 2017-12-05 11:38 211M chainCanFam3.sql 2017-12-05 11:39 1.7K chainCanFam3.txt.gz 2017-12-05 11:39 46M chainCanFam3Link.sql 2017-12-05 11:39 1.5K chainCanFam3Link.txt.gz 2017-12-05 11:39 187M chainFr3.sql 2017-12-05 11:40 1.7K chainFr3.txt.gz 2017-12-05 11:40 12M chainFr3Link.sql 2017-12-05 11:40 1.5K chainFr3Link.txt.gz 2017-12-05 11:40 49M chainGalGal5.sql 2017-12-05 11:40 1.7K chainGalGal5.txt.gz 2017-12-05 11:40 6.7M chainGalGal5Link.sql 2017-12-05 11:40 1.5K chainGalGal5Link.txt.gz 2017-12-05 11:40 25M chainGalGal6.sql 2019-01-20 20:25 1.7K chainGalGal6.txt.gz 2019-01-20 20:25 24M chainGalGal6Link.sql 2019-01-20 20:25 1.5K chainGalGal6Link.txt.gz 2019-01-20 20:26 101M chainHg38.sql 2017-12-05 11:41 1.7K chainHg38.txt.gz 2017-12-05 11:41 229M chainHg38Link.sql 2017-12-05 11:42 1.5K chainHg38Link.txt.gz 2017-12-05 11:43 1.0G chainMm10.sql 2017-12-05 11:47 1.7K chainMm10.txt.gz 2017-12-05 11:47 67M chainMm10Link.sql 2017-12-05 11:47 1.5K chainMm10Link.txt.gz 2017-12-05 11:47 401M chainMm39.sql 2020-11-25 03:44 1.7K chainMm39.txt.gz 2020-11-25 03:44 35M chainMm39Link.sql 2020-11-25 03:45 1.6K chainMm39Link.txt.gz 2020-11-25 03:45 175M chainMonDom5.sql 2017-12-05 11:32 1.7K chainMonDom5.txt.gz 2017-12-05 11:33 224M chainMonDom5Link.sql 2017-12-05 11:33 1.5K chainMonDom5Link.txt.gz 2017-12-05 11:34 812M chainNanPar1.sql 2017-12-05 11:37 1.7K chainNanPar1.txt.gz 2017-12-05 11:37 97M chainNanPar1Link.sql 2017-12-05 11:49 1.5K chainNanPar1Link.txt.gz 2017-12-05 11:49 293M chainXenLae2.sql 2017-12-05 11:05 1.7K chainXenLae2.txt.gz 2017-12-05 11:07 1.8G chainXenLae2Link.sql 2017-12-05 11:13 1.5K chainXenLae2Link.txt.gz 2017-12-05 11:18 3.9G chromAlias.sql 2020-04-12 03:26 1.4K chromAlias.txt.gz 2020-04-12 03:26 67K chromInfo.sql 2017-12-05 11:50 1.4K chromInfo.txt.gz 2017-12-05 11:50 35K cpgIslandExt.sql 2017-12-05 11:39 1.7K cpgIslandExt.txt.gz 2017-12-05 11:39 274K cpgIslandExtUnmasked.sql 2017-12-05 11:39 1.7K cpgIslandExtUnmasked.txt.gz 2017-12-05 11:39 888K cytoBandIdeo.sql 2017-12-05 11:40 1.5K cytoBandIdeo.txt.gz 2017-12-05 11:40 36K ensGene.sql 2020-08-31 16:05 1.9K ensGene.txt.gz 2020-08-31 16:05 3.4M ensGtp.sql 2020-08-31 16:05 1.4K ensGtp.txt.gz 2020-08-31 16:05 556K ensPep.sql 2020-09-01 00:32 1.3K ensPep.txt.gz 2020-09-01 00:32 22M ensemblSource.sql 2020-09-01 00:32 1.4K ensemblSource.txt.gz 2020-09-01 00:32 155K ensemblToGeneName.sql 2020-08-31 16:05 1.4K ensemblToGeneName.txt.gz 2020-08-31 16:05 332K estOrientInfo.sql 2017-12-05 11:40 1.8K estOrientInfo.txt.gz 2017-12-05 11:40 14M extFile.sql 2017-12-05 11:40 1.4K extFile.txt.gz 2017-12-05 11:40 80 extNcbiRefSeq.sql 2021-02-11 11:15 1.5K extNcbiRefSeq.txt.gz 2021-02-11 11:15 91 gap.sql 2017-12-05 11:42 1.6K gap.txt.gz 2017-12-05 11:42 714K gbLoaded.sql 2020-08-20 19:13 1.6K gbLoaded.txt.gz 2020-08-20 19:13 32K gc5BaseBw.sql 2017-12-05 11:47 1.3K gc5BaseBw.txt.gz 2017-12-05 11:47 66 genscan.sql 2017-12-05 11:50 1.7K genscan.txt.gz 2017-12-05 11:50 2.3M gold.sql 2017-12-05 11:32 1.7K gold.txt.gz 2017-12-05 11:32 1.0M grp.sql 2017-12-05 11:32 1.3K grp.txt.gz 2017-12-05 11:32 213 hgFindSpec.sql 2021-03-26 09:06 1.8K hgFindSpec.txt.gz 2021-03-26 09:06 1.2K history.sql 2017-12-05 11:40 1.6K history.txt.gz 2017-12-05 11:40 1.4K intronEst.sql 2017-12-05 11:40 2.1K intronEst.txt.gz 2017-12-05 11:40 32M microsat.sql 2017-12-05 11:47 1.5K microsat.txt.gz 2017-12-05 11:47 145K mrnaOrientInfo.sql 2020-08-20 19:13 1.8K mrnaOrientInfo.txt.gz 2020-08-20 19:13 509K multiz11way.sql 2017-12-05 11:50 1.5K multiz11way.txt.gz 2017-12-05 11:50 53M multiz11wayFrames.sql 2017-12-05 11:51 1.7K multiz11wayFrames.txt.gz 2017-12-05 11:51 11M multiz11waySummary.sql 2017-12-05 11:51 1.6K multiz11waySummary.txt.gz 2017-12-05 11:51 8.9M ncbiRefSeq.sql 2021-02-11 09:53 2.0K ncbiRefSeq.txt.gz 2021-02-11 09:53 2.8M ncbiRefSeqCds.sql 2021-02-11 11:15 1.4K ncbiRefSeqCds.txt.gz 2021-02-11 11:15 277K ncbiRefSeqCurated.sql 2021-02-11 09:53 2.0K ncbiRefSeqCurated.txt.gz 2021-02-11 09:53 877K ncbiRefSeqLink.sql 2021-02-11 09:53 2.0K ncbiRefSeqLink.txt.gz 2021-02-11 09:53 1.6M ncbiRefSeqOther.sql 2021-02-11 11:15 1.3K ncbiRefSeqOther.txt.gz 2021-02-11 11:15 75 ncbiRefSeqPepTable.sql 2021-02-11 11:15 1.4K ncbiRefSeqPepTable.txt.gz 2021-02-11 11:15 10M ncbiRefSeqPredicted.sql 2021-02-11 09:53 2.0K ncbiRefSeqPredicted.txt.gz 2021-02-11 09:53 2.3M ncbiRefSeqPsl.sql 2021-02-11 09:53 2.1K ncbiRefSeqPsl.txt.gz 2021-02-11 09:53 3.5M nestedRepeats.sql 2017-12-05 11:51 1.9K nestedRepeats.txt.gz 2017-12-05 11:51 4.5M netAnoCar2.sql 2017-12-05 11:51 2.1K netAnoCar2.txt.gz 2017-12-05 11:51 8.2M netCanFam3.sql 2017-12-05 11:51 2.1K netCanFam3.txt.gz 2017-12-05 11:51 5.7M netFr3.sql 2017-12-05 11:51 2.1K netFr3.txt.gz 2017-12-05 11:51 5.8M netGalGal5.sql 2017-12-05 11:51 2.1K netGalGal5.txt.gz 2017-12-05 11:51 5.5M netGalGal6.sql 2019-01-20 20:26 2.1K netGalGal6.txt.gz 2019-01-20 20:26 9.8M netHg38.sql 2017-12-05 11:51 2.1K netHg38.txt.gz 2017-12-05 11:51 11M netMm10.sql 2017-12-05 11:51 2.1K netMm10.txt.gz 2017-12-05 11:51 9.2M netMm39.sql 2020-11-25 03:47 2.1K netMm39.txt.gz 2020-11-25 03:47 6.5M netMonDom5.sql 2017-12-05 11:51 2.1K netMonDom5.txt.gz 2017-12-05 11:51 7.3M netNanPar1.sql 2017-12-05 11:51 2.1K netNanPar1.txt.gz 2017-12-05 11:51 12M netXenLae2.sql 2017-12-05 11:32 2.1K netXenLae2.txt.gz 2017-12-05 11:32 89M phastCons11way.sql 2017-12-05 11:51 1.8K phastCons11way.txt.gz 2017-12-05 11:51 32M phastConsElements11way.sql 2017-12-05 11:52 1.6K phastConsElements11way.txt.gz 2017-12-05 11:52 6.8M phyloP11way.sql 2017-12-05 11:52 1.8K phyloP11way.txt.gz 2017-12-05 11:52 32M refFlat.sql 2020-08-20 19:07 1.7K refFlat.txt.gz 2020-08-20 19:07 824K refGene.sql 2020-08-20 19:07 1.9K refGene.txt.gz 2020-08-20 19:07 921K refSeqAli.sql 2020-08-20 19:13 2.1K refSeqAli.txt.gz 2020-08-20 19:13 932K rmsk.sql 2017-12-05 11:52 1.9K rmsk.txt.gz 2017-12-05 11:52 58M seqNcbiRefSeq.sql 2021-02-11 11:15 1.6K seqNcbiRefSeq.txt.gz 2021-02-11 11:15 662K simpleRepeat.sql 2017-12-05 11:52 1.9K simpleRepeat.txt.gz 2017-12-05 11:52 19M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K tableList.sql 2021-05-02 03:04 1.6K tableList.txt.gz 2021-05-02 03:04 4.9K trackDb.sql 2021-03-26 09:06 2.1K trackDb.txt.gz 2021-03-26 09:06 57K ucscToINSDC.sql 2017-12-05 11:52 1.4K ucscToINSDC.txt.gz 2017-12-05 11:52 51K ucscToRefSeq.sql 2017-12-05 11:52 1.4K ucscToRefSeq.txt.gz 2017-12-05 11:52 55K windowmaskerSdust.sql 2017-12-05 11:51 1.5K windowmaskerSdust.txt.gz 2017-12-05 11:51 63M xenoRefFlat.sql 2020-08-20 19:07 1.7K xenoRefFlat.txt.gz 2020-08-20 19:07 14M xenoRefGene.sql 2020-08-20 19:07 1.9K xenoRefGene.txt.gz 2020-08-20 19:07 16M xenoRefSeqAli.sql 2020-08-20 19:13 2.1K xenoRefSeqAli.txt.gz 2020-08-20 19:13 13M