This directory contains a dump of the UCSC genome annotation database for the
    Aug. 2016 (Xenopus_laevis_v2/xenLae2) assembly of the african clawed frog genome
    (xenLae2, International Xenopus Sequencing 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/81
    http://www.ncbi.nlm.nih.gov/genome/assembly/779791
    http://www.ncbi.nlm.nih.gov/bioproject/338693

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=xenLae2
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/xenLae2/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/xenLae2/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/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 xenLae2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenLae2 --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 - augustusGene.sql 2017-11-15 13:09 1.9K augustusGene.txt.gz 2017-11-15 13:09 3.4M rmsk.sql 2017-11-15 13:09 1.9K rmsk.txt.gz 2017-11-15 13:09 44M chainHg38.sql 2017-11-15 13:09 1.7K chainHg38.txt.gz 2017-11-15 13:09 63M chainHg38Link.sql 2017-11-15 13:10 1.5K history.sql 2017-11-15 13:10 1.6K history.txt.gz 2017-11-15 13:10 655 chainHg38Link.txt.gz 2017-11-15 13:10 291M simpleRepeat.sql 2017-11-15 13:11 1.9K simpleRepeat.txt.gz 2017-11-15 13:11 21M chainMm10.sql 2017-11-15 13:11 1.7K chainMm10.txt.gz 2017-11-15 13:11 33M chainMm10Link.sql 2017-11-15 13:11 1.5K chainMm10Link.txt.gz 2017-11-15 13:12 290M chainXenTro9.sql 2017-11-15 13:13 1.7K microsat.sql 2017-11-15 13:13 1.5K microsat.txt.gz 2017-11-15 13:13 105K chainXenTro9.txt.gz 2017-11-15 13:15 1.6G chainXenTro9Link.sql 2017-11-15 13:20 1.5K chainXenTro9Link.txt.gz 2017-11-15 13:25 3.5G nestedRepeats.sql 2017-11-15 13:38 1.9K nestedRepeats.txt.gz 2017-11-15 13:38 2.9M chromAlias.sql 2017-11-15 13:38 1.4K chromAlias.txt.gz 2017-11-15 13:38 1.0M chromInfo.sql 2017-11-15 13:38 1.4K chromInfo.txt.gz 2017-11-15 13:38 346K netHg38.sql 2017-11-15 13:38 2.1K netHg38.txt.gz 2017-11-15 13:38 12M cpgIslandExt.sql 2017-11-15 13:38 1.7K cpgIslandExt.txt.gz 2017-11-15 13:38 262K cpgIslandExtUnmasked.sql 2017-11-15 13:38 1.7K cpgIslandExtUnmasked.txt.gz 2017-11-15 13:38 1.7M genscan.sql 2017-11-15 13:38 1.7K genscan.txt.gz 2017-11-15 13:38 2.9M netMm10.sql 2017-11-15 13:38 2.1K netMm10.txt.gz 2017-11-15 13:38 12M cytoBandIdeo.sql 2017-11-15 13:38 1.5K cytoBandIdeo.txt.gz 2017-11-15 13:38 271K netXenTro9.sql 2017-11-15 13:38 2.1K netXenTro9.txt.gz 2017-11-15 13:38 111M gap.sql 2017-11-15 13:39 1.6K gap.txt.gz 2017-11-15 13:39 3.0M ucscToINSDC.sql 2017-11-15 13:39 1.4K ucscToINSDC.txt.gz 2017-11-15 13:39 551K gc5BaseBw.sql 2017-11-15 13:39 1.3K gc5BaseBw.txt.gz 2017-11-15 13:39 66 gold.sql 2017-11-15 13:39 1.7K gold.txt.gz 2017-11-15 13:39 4.4M ucscToRefSeq.sql 2017-11-15 13:39 1.4K ucscToRefSeq.txt.gz 2017-11-15 13:39 549K windowmaskerSdust.sql 2017-11-15 13:39 1.5K windowmaskerSdust.txt.gz 2017-11-15 13:39 129M grp.sql 2017-11-15 13:39 1.3K grp.txt.gz 2017-11-15 13:39 213 all_est.sql 2018-10-21 09:23 2.1K all_est.txt.gz 2018-10-21 09:23 38M intronEst.sql 2018-10-21 09:24 2.1K intronEst.txt.gz 2018-10-21 09:24 25M estOrientInfo.sql 2018-10-21 09:24 1.8K estOrientInfo.txt.gz 2018-10-21 09:24 8.8M netGalGal6.sql 2019-01-20 20:25 2.1K netGalGal6.txt.gz 2019-01-20 20:25 13M chainGalGal6.sql 2019-01-20 20:25 1.7K chainGalGal6.txt.gz 2019-01-20 20:25 12M chainGalGal6Link.sql 2019-01-20 20:25 1.5K chainGalGal6Link.txt.gz 2019-01-20 20:25 65M tableDescriptions.sql 2020-04-26 03:23 1.4K tableDescriptions.txt.gz 2020-04-26 03:23 6.2K extNcbiRefSeq.sql 2020-05-10 03:29 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:29 91 ncbiRefSeq.sql 2020-05-10 03:29 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:29 4.2M ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:29 386K ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 1.1M ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.9M ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75 ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 12M ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 3.4M ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 5.3M seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:29 921K all_mrna.sql 2020-08-20 18:26 2.1K all_mrna.txt.gz 2020-08-20 18:26 2.0M refGene.sql 2020-08-20 18:30 1.9K refGene.txt.gz 2020-08-20 18:30 1.2M refFlat.sql 2020-08-20 18:42 1.7K xenoRefGene.sql 2020-08-20 18:42 1.9K refFlat.txt.gz 2020-08-20 18:42 1.1M xenoRefGene.txt.gz 2020-08-20 18:42 21M xenoRefFlat.sql 2020-08-20 18:44 1.7K xenoRefFlat.txt.gz 2020-08-20 18:44 18M gbLoaded.sql 2020-08-20 18:44 1.6K mrnaOrientInfo.sql 2020-08-20 18:44 1.8K refSeqAli.sql 2020-08-20 18:44 2.1K xenoRefSeqAli.sql 2020-08-20 18:44 2.1K mrnaOrientInfo.txt.gz 2020-08-20 18:44 611K refSeqAli.txt.gz 2020-08-20 18:44 1.2M xenoRefSeqAli.txt.gz 2020-08-20 18:44 18M gbLoaded.txt.gz 2020-08-20 18:44 32K trackDb.sql 2021-06-10 16:56 2.1K trackDb.txt.gz 2021-06-10 16:56 42K hgFindSpec.sql 2021-06-10 16:56 1.8K hgFindSpec.txt.gz 2021-06-10 16:56 1.0K bigFiles.sql 2021-06-13 03:04 1.4K bigFiles.txt.gz 2021-06-13 03:04 95 tableList.sql 2021-06-13 03:04 1.6K tableList.txt.gz 2021-06-13 03:04 3.4K