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.
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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 -
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
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
refFlat.txt.gz 2020-08-20 18:42 1.1M
xenoRefGene.sql 2020-08-20 18:42 2.0K
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
mrnaOrientInfo.sql 2020-08-20 18:44 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 18:44 611K
refSeqAli.sql 2020-08-20 18:44 2.1K
refSeqAli.txt.gz 2020-08-20 18:44 1.2M
xenoRefSeqAli.sql 2020-08-20 18:44 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 18:44 18M
gbLoaded.sql 2020-08-20 18:44 1.6K
gbLoaded.txt.gz 2020-08-20 18:44 32K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 34K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:52 34K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.1K
tableDescriptions.sql 2024-04-13 02:04 1.5K
tableDescriptions.txt.gz 2024-04-13 02:04 6.3K
tableList.sql 2024-04-14 03:06 1.6K
tableList.txt.gz 2024-04-14 03:06 3.6K
bigFiles.sql 2024-04-14 03:06 1.4K
bigFiles.txt.gz 2024-04-14 03:06 95