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 - gc5BaseBw.txt.gz 2017-12-05 11:47 66 ncbiRefSeqOther.txt.gz 2021-02-11 11:15 75 extFile.txt.gz 2017-12-05 11:40 80 extNcbiRefSeq.txt.gz 2021-02-11 11:15 91 bigFiles.txt.gz 2022-08-14 03:04 95 grp.txt.gz 2017-12-05 11:32 213 hgFindSpec.txt.gz 2021-12-27 12:23 1.2K gc5BaseBw.sql 2017-12-05 11:47 1.3K ncbiRefSeqOther.sql 2021-02-11 11:15 1.3K ensPep.sql 2021-05-25 14:10 1.3K grp.sql 2017-12-05 11:32 1.3K ncbiRefSeqCds.sql 2021-02-11 11:15 1.4K bigFiles.sql 2022-08-14 03:04 1.4K ensemblSource.sql 2021-05-25 14:10 1.4K ncbiRefSeqPepTable.sql 2021-02-11 11:15 1.4K history.txt.gz 2017-12-05 11:40 1.4K chromInfo.sql 2017-12-05 11:50 1.4K ensemblToGeneName.sql 2021-05-25 14:04 1.4K extFile.sql 2017-12-05 11:40 1.4K chromAlias.sql 2020-04-12 03:26 1.4K tableDescriptions.sql 2021-03-13 06:37 1.4K ucscToINSDC.sql 2017-12-05 11:52 1.4K ucscToRefSeq.sql 2017-12-05 11:52 1.4K ensGtp.sql 2021-05-25 14:04 1.4K extNcbiRefSeq.sql 2021-02-11 11:15 1.5K microsat.sql 2017-12-05 11:47 1.5K windowmaskerSdust.sql 2017-12-05 11:51 1.5K cytoBandIdeo.sql 2017-12-05 11:40 1.5K multiz11way.sql 2017-12-05 11:50 1.5K chainFr3Link.sql 2017-12-05 11:40 1.5K chainHg38Link.sql 2017-12-05 11:42 1.5K chainMm10Link.sql 2017-12-05 11:47 1.5K chainAnoCar2Link.sql 2017-12-05 11:38 1.5K chainCanFam3Link.sql 2017-12-05 11:39 1.5K chainGalGal5Link.sql 2017-12-05 11:40 1.5K chainGalGal6Link.sql 2019-01-20 20:25 1.5K chainMonDom5Link.sql 2017-12-05 11:33 1.5K chainNanPar1Link.sql 2017-12-05 11:49 1.5K chainXenLae2Link.sql 2017-12-05 11:13 1.5K chainMm39Link.sql 2020-11-25 03:45 1.6K tableList.sql 2022-08-14 03:04 1.6K phastConsElements11way.sql 2017-12-05 11:52 1.6K seqNcbiRefSeq.sql 2021-02-11 11:15 1.6K history.sql 2017-12-05 11:40 1.6K gbLoaded.sql 2020-08-20 19:13 1.6K multiz11waySummary.sql 2017-12-05 11:51 1.6K gap.sql 2017-12-05 11:42 1.6K gold.sql 2017-12-05 11:32 1.7K genscan.sql 2017-12-05 11:50 1.7K cpgIslandExt.sql 2017-12-05 11:39 1.7K chainFr3.sql 2017-12-05 11:40 1.7K chainHg38.sql 2017-12-05 11:41 1.7K chainMm10.sql 2017-12-05 11:47 1.7K refFlat.sql 2020-08-20 19:07 1.7K chainAnoCar2.sql 2017-12-05 11:37 1.7K chainCanFam3.sql 2017-12-05 11:39 1.7K chainGalGal5.sql 2017-12-05 11:40 1.7K chainGalGal6.sql 2019-01-20 20:25 1.7K chainMonDom5.sql 2017-12-05 11:32 1.7K chainNanPar1.sql 2017-12-05 11:37 1.7K chainXenLae2.sql 2017-12-05 11:05 1.7K cpgIslandExtUnmasked.sql 2017-12-05 11:39 1.7K xenoRefFlat.sql 2020-08-20 19:07 1.7K chainMm39.sql 2020-11-25 03:44 1.7K multiz11wayFrames.sql 2017-12-05 11:51 1.7K hgFindSpec.sql 2021-12-27 12:23 1.8K phyloP11way.sql 2017-12-05 11:52 1.8K estOrientInfo.sql 2017-12-05 11:40 1.8K mrnaOrientInfo.sql 2020-08-20 19:13 1.8K phastCons11way.sql 2017-12-05 11:51 1.8K rmsk.sql 2017-12-05 11:52 1.9K refGene.sql 2020-08-20 19:07 1.9K simpleRepeat.sql 2017-12-05 11:52 1.9K nestedRepeats.sql 2017-12-05 11:51 1.9K xenoRefGene.sql 2020-08-20 19:07 1.9K augustusGene.sql 2017-12-05 11:33 1.9K ensGene.sql 2021-05-25 14:04 1.9K ncbiRefSeq.sql 2021-02-11 09:53 2.0K ncbiRefSeqCurated.sql 2021-02-11 09:53 2.0K ncbiRefSeqPredicted.sql 2021-02-11 09:53 2.0K ncbiRefSeqLink.sql 2021-02-11 09:53 2.0K trackDb.sql 2021-12-27 12:23 2.1K netFr3.sql 2017-12-05 11:51 2.1K netHg38.sql 2017-12-05 11:51 2.1K netMm10.sql 2017-12-05 11:51 2.1K netAnoCar2.sql 2017-12-05 11:51 2.1K netCanFam3.sql 2017-12-05 11:51 2.1K netGalGal5.sql 2017-12-05 11:51 2.1K netGalGal6.sql 2019-01-20 20:26 2.1K netMonDom5.sql 2017-12-05 11:51 2.1K netNanPar1.sql 2017-12-05 11:51 2.1K netXenLae2.sql 2017-12-05 11:32 2.1K all_est.sql 2017-12-05 11:32 2.1K all_mrna.sql 2020-08-20 18:44 2.1K intronEst.sql 2017-12-05 11:40 2.1K refSeqAli.sql 2020-08-20 19:13 2.1K netMm39.sql 2020-11-25 03:47 2.1K xenoRefSeqAli.sql 2020-08-20 19:13 2.1K ncbiRefSeqPsl.sql 2021-02-11 09:53 2.1K tableList.txt.gz 2022-08-14 03:04 4.9K tableDescriptions.txt.gz 2021-03-13 06:37 7.6K gbLoaded.txt.gz 2020-08-20 19:13 32K chromInfo.txt.gz 2017-12-05 11:50 35K cytoBandIdeo.txt.gz 2017-12-05 11:40 36K ucscToINSDC.txt.gz 2017-12-05 11:52 51K ucscToRefSeq.txt.gz 2017-12-05 11:52 55K trackDb.txt.gz 2021-12-27 12:23 59K chromAlias.txt.gz 2020-04-12 03:26 67K microsat.txt.gz 2017-12-05 11:47 145K ensemblSource.txt.gz 2021-05-25 14:10 155K cpgIslandExt.txt.gz 2017-12-05 11:39 274K ncbiRefSeqCds.txt.gz 2021-02-11 11:15 277K ensemblToGeneName.txt.gz 2021-05-25 14:04 334K mrnaOrientInfo.txt.gz 2020-08-20 19:13 509K ensGtp.txt.gz 2021-05-25 14:04 561K seqNcbiRefSeq.txt.gz 2021-02-11 11:15 662K gap.txt.gz 2017-12-05 11:42 714K refFlat.txt.gz 2020-08-20 19:07 824K ncbiRefSeqCurated.txt.gz 2021-02-11 09:53 877K cpgIslandExtUnmasked.txt.gz 2017-12-05 11:39 888K refGene.txt.gz 2020-08-20 19:07 921K refSeqAli.txt.gz 2020-08-20 19:13 932K gold.txt.gz 2017-12-05 11:32 1.0M ncbiRefSeqLink.txt.gz 2021-02-11 09:53 1.6M all_mrna.txt.gz 2020-08-20 18:44 1.8M augustusGene.txt.gz 2017-12-05 11:33 2.2M ncbiRefSeqPredicted.txt.gz 2021-02-11 09:53 2.3M genscan.txt.gz 2017-12-05 11:50 2.3M ncbiRefSeq.txt.gz 2021-02-11 09:53 2.8M ensGene.txt.gz 2021-05-25 14:04 3.4M ncbiRefSeqPsl.txt.gz 2021-02-11 09:53 3.5M nestedRepeats.txt.gz 2017-12-05 11:51 4.5M netGalGal5.txt.gz 2017-12-05 11:51 5.5M netCanFam3.txt.gz 2017-12-05 11:51 5.7M netFr3.txt.gz 2017-12-05 11:51 5.8M netMm39.txt.gz 2020-11-25 03:47 6.5M chainGalGal5.txt.gz 2017-12-05 11:40 6.7M phastConsElements11way.txt.gz 2017-12-05 11:52 6.8M netMonDom5.txt.gz 2017-12-05 11:51 7.3M netAnoCar2.txt.gz 2017-12-05 11:51 8.2M multiz11waySummary.txt.gz 2017-12-05 11:51 8.9M netMm10.txt.gz 2017-12-05 11:51 9.2M netGalGal6.txt.gz 2019-01-20 20:26 9.8M ncbiRefSeqPepTable.txt.gz 2021-02-11 11:15 10M multiz11wayFrames.txt.gz 2017-12-05 11:51 11M netHg38.txt.gz 2017-12-05 11:51 11M chainFr3.txt.gz 2017-12-05 11:40 12M netNanPar1.txt.gz 2017-12-05 11:51 12M xenoRefSeqAli.txt.gz 2020-08-20 19:13 13M xenoRefFlat.txt.gz 2020-08-20 19:07 14M estOrientInfo.txt.gz 2017-12-05 11:40 14M xenoRefGene.txt.gz 2020-08-20 19:07 16M simpleRepeat.txt.gz 2017-12-05 11:52 19M ensPep.txt.gz 2021-05-25 14:10 22M chainGalGal6.txt.gz 2019-01-20 20:25 24M chainGalGal5Link.txt.gz 2017-12-05 11:40 25M phyloP11way.txt.gz 2017-12-05 11:52 32M intronEst.txt.gz 2017-12-05 11:40 32M phastCons11way.txt.gz 2017-12-05 11:51 32M chainMm39.txt.gz 2020-11-25 03:44 35M chainAnoCar2.txt.gz 2017-12-05 11:37 45M chainCanFam3.txt.gz 2017-12-05 11:39 46M chainFr3Link.txt.gz 2017-12-05 11:40 49M all_est.txt.gz 2017-12-05 11:32 51M multiz11way.txt.gz 2017-12-05 11:50 53M rmsk.txt.gz 2017-12-05 11:52 58M windowmaskerSdust.txt.gz 2017-12-05 11:51 63M chainMm10.txt.gz 2017-12-05 11:47 67M netXenLae2.txt.gz 2017-12-05 11:32 89M chainNanPar1.txt.gz 2017-12-05 11:37 97M chainGalGal6Link.txt.gz 2019-01-20 20:26 101M chainMm39Link.txt.gz 2020-11-25 03:45 175M chainCanFam3Link.txt.gz 2017-12-05 11:39 187M chainAnoCar2Link.txt.gz 2017-12-05 11:38 211M chainMonDom5.txt.gz 2017-12-05 11:33 224M chainHg38.txt.gz 2017-12-05 11:41 229M chainNanPar1Link.txt.gz 2017-12-05 11:49 293M chainMm10Link.txt.gz 2017-12-05 11:47 401M chainMonDom5Link.txt.gz 2017-12-05 11:34 812M chainHg38Link.txt.gz 2017-12-05 11:43 1.0G chainXenLae2.txt.gz 2017-12-05 11:07 1.8G chainXenLae2Link.txt.gz 2017-12-05 11:18 3.9G