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 - 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 netXenLae2.sql 2017-12-05 11:32 2.1K netXenLae2.txt.gz 2017-12-05 11:32 89M gold.sql 2017-12-05 11:32 1.7K gold.txt.gz 2017-12-05 11:32 1.0M all_est.sql 2017-12-05 11:32 2.1K all_est.txt.gz 2017-12-05 11:32 51M grp.sql 2017-12-05 11:32 1.3K grp.txt.gz 2017-12-05 11:32 213 chainMonDom5.sql 2017-12-05 11:32 1.7K chainMonDom5.txt.gz 2017-12-05 11:33 224M augustusGene.sql 2017-12-05 11:33 1.9K augustusGene.txt.gz 2017-12-05 11:33 2.2M chainMonDom5Link.sql 2017-12-05 11:33 1.5K chainMonDom5Link.txt.gz 2017-12-05 11:34 812M chainAnoCar2.sql 2017-12-05 11:37 1.7K chainAnoCar2.txt.gz 2017-12-05 11:37 45M chainNanPar1.sql 2017-12-05 11:37 1.7K chainNanPar1.txt.gz 2017-12-05 11:37 97M 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 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 chainCanFam3Link.sql 2017-12-05 11:39 1.5K cpgIslandExtUnmasked.txt.gz 2017-12-05 11:39 888K 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 history.sql 2017-12-05 11:40 1.6K history.txt.gz 2017-12-05 11:40 1.4K chainFr3Link.sql 2017-12-05 11:40 1.5K cytoBandIdeo.sql 2017-12-05 11:40 1.5K cytoBandIdeo.txt.gz 2017-12-05 11:40 36K chainFr3Link.txt.gz 2017-12-05 11:40 49M estOrientInfo.sql 2017-12-05 11:40 1.8K estOrientInfo.txt.gz 2017-12-05 11:40 14M 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 extFile.sql 2017-12-05 11:40 1.4K extFile.txt.gz 2017-12-05 11:40 80 chainGalGal5Link.txt.gz 2017-12-05 11:40 25M intronEst.sql 2017-12-05 11:40 2.1K intronEst.txt.gz 2017-12-05 11:40 32M 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 gap.sql 2017-12-05 11:42 1.6K gap.txt.gz 2017-12-05 11:42 714K chainHg38Link.txt.gz 2017-12-05 11:43 1.0G chainMm10.sql 2017-12-05 11:47 1.7K microsat.sql 2017-12-05 11:47 1.5K microsat.txt.gz 2017-12-05 11:47 145K chainMm10.txt.gz 2017-12-05 11:47 67M chainMm10Link.sql 2017-12-05 11:47 1.5K gc5BaseBw.sql 2017-12-05 11:47 1.3K gc5BaseBw.txt.gz 2017-12-05 11:47 66 chainMm10Link.txt.gz 2017-12-05 11:47 401M chainNanPar1Link.sql 2017-12-05 11:49 1.5K chainNanPar1Link.txt.gz 2017-12-05 11:49 293M genscan.sql 2017-12-05 11:50 1.7K genscan.txt.gz 2017-12-05 11:50 2.3M chromInfo.sql 2017-12-05 11:50 1.4K chromInfo.txt.gz 2017-12-05 11:50 35K 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 windowmaskerSdust.sql 2017-12-05 11:51 1.5K windowmaskerSdust.txt.gz 2017-12-05 11:51 63M 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 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 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 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 ucscToRefSeq.sql 2017-12-05 11:52 1.4K ucscToRefSeq.txt.gz 2017-12-05 11:52 55K 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 rmsk.sql 2017-12-05 11:52 1.9K rmsk.txt.gz 2017-12-05 11:52 58M simpleRepeat.sql 2017-12-05 11:52 1.9K simpleRepeat.txt.gz 2017-12-05 11:52 19M ucscToINSDC.sql 2017-12-05 11:52 1.4K ucscToINSDC.txt.gz 2017-12-05 11:52 51K 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 netGalGal6.sql 2019-01-20 20:26 2.1K netGalGal6.txt.gz 2019-01-20 20:26 9.8M chromAlias.sql 2020-04-12 03:26 1.4K chromAlias.txt.gz 2020-04-12 03:26 67K all_mrna.sql 2020-08-20 18:44 2.1K all_mrna.txt.gz 2020-08-20 18:44 1.8M refFlat.sql 2020-08-20 19:07 1.7K refGene.sql 2020-08-20 19:07 1.9K xenoRefFlat.sql 2020-08-20 19:07 1.7K xenoRefGene.sql 2020-08-20 19:07 1.9K refGene.txt.gz 2020-08-20 19:07 921K refFlat.txt.gz 2020-08-20 19:07 824K xenoRefGene.txt.gz 2020-08-20 19:07 16M xenoRefFlat.txt.gz 2020-08-20 19:07 14M mrnaOrientInfo.sql 2020-08-20 19:13 1.8K mrnaOrientInfo.txt.gz 2020-08-20 19:13 509K refSeqAli.sql 2020-08-20 19:13 2.1K refSeqAli.txt.gz 2020-08-20 19:13 932K xenoRefSeqAli.sql 2020-08-20 19:13 2.1K xenoRefSeqAli.txt.gz 2020-08-20 19:13 13M gbLoaded.sql 2020-08-20 19:13 1.6K gbLoaded.txt.gz 2020-08-20 19:13 32K 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 netMm39.sql 2020-11-25 03:47 2.1K netMm39.txt.gz 2020-11-25 03:47 6.5M ncbiRefSeq.sql 2021-02-11 09:53 2.0K ncbiRefSeq.txt.gz 2021-02-11 09:53 2.8M ncbiRefSeqCurated.sql 2021-02-11 09:53 2.0K ncbiRefSeqCurated.txt.gz 2021-02-11 09:53 877K ncbiRefSeqPredicted.sql 2021-02-11 09:53 2.0K ncbiRefSeqPredicted.txt.gz 2021-02-11 09:53 2.3M ncbiRefSeqLink.sql 2021-02-11 09:53 2.0K ncbiRefSeqLink.txt.gz 2021-02-11 09:53 1.6M ncbiRefSeqPsl.sql 2021-02-11 09:53 2.1K ncbiRefSeqPsl.txt.gz 2021-02-11 09:53 3.5M ncbiRefSeqOther.sql 2021-02-11 11:15 1.3K ncbiRefSeqOther.txt.gz 2021-02-11 11:15 75 ncbiRefSeqCds.sql 2021-02-11 11:15 1.4K ncbiRefSeqCds.txt.gz 2021-02-11 11:15 277K ncbiRefSeqPepTable.sql 2021-02-11 11:15 1.4K ncbiRefSeqPepTable.txt.gz 2021-02-11 11:15 10M extNcbiRefSeq.sql 2021-02-11 11:15 1.5K extNcbiRefSeq.txt.gz 2021-02-11 11:15 91 seqNcbiRefSeq.sql 2021-02-11 11:15 1.6K seqNcbiRefSeq.txt.gz 2021-02-11 11:15 662K tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K ensGene.sql 2021-05-25 14:04 1.9K ensGene.txt.gz 2021-05-25 14:04 3.4M ensGtp.sql 2021-05-25 14:04 1.4K ensGtp.txt.gz 2021-05-25 14:04 561K ensemblToGeneName.sql 2021-05-25 14:04 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:04 334K ensemblSource.sql 2021-05-25 14:10 1.4K ensemblSource.txt.gz 2021-05-25 14:10 155K ensPep.sql 2021-05-25 14:10 1.3K ensPep.txt.gz 2021-05-25 14:10 22M trackDb.sql 2021-12-27 12:23 2.1K trackDb.txt.gz 2021-12-27 12:23 59K hgFindSpec.sql 2021-12-27 12:23 1.8K hgFindSpec.txt.gz 2021-12-27 12:23 1.2K tableList.sql 2022-08-14 03:04 1.6K tableList.txt.gz 2022-08-14 03:04 4.9K bigFiles.sql 2022-08-14 03:04 1.4K bigFiles.txt.gz 2022-08-14 03:04 95