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;'

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