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