This directory contains a dump of the UCSC genome annotation database for the
Sep. 2012 (JGI 7.0/xenTro7) assembly of the X. tropicalis genome
(xenTro7, US DOE Joint Genome Institute (JGI-PGF))
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/assembly/515038
http://www.ncbi.nlm.nih.gov/bioproject/12348
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=xenTro7
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.cse.ucsc.edu, then go to
the directory goldenPath/xenTro7/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.cse.ucsc.edu/goldenPath/xenTro7/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/xenTro7/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
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 xenTro7 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro7 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
1. The data may be freely downloaded, used in analyses, and repackaged
in databases.
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the provider of these data
(DOE Joint Genome Institute) is properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. Any redistribution of the data should carry this notice.
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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 -
all_est.sql 2015-12-21 09:55 2.1K
all_est.txt.gz 2015-12-21 09:55 52M
all_mrna.sql 2020-05-11 17:36 2.1K
all_mrna.txt.gz 2020-05-11 17:36 1.9M
augustusGene.sql 2015-12-21 09:56 1.9K
augustusGene.txt.gz 2015-12-21 09:56 2.2M
bigFiles.sql 2024-11-17 03:39 1.4K
bigFiles.txt.gz 2024-11-17 03:39 94
chainHg38.sql 2015-12-21 09:56 1.7K
chainHg38.txt.gz 2015-12-21 09:56 229M
chainHg38Link.sql 2015-12-21 09:57 1.5K
chainHg38Link.txt.gz 2015-12-21 09:58 1.0G
chainMelGal5.sql 2017-03-21 07:23 1.7K
chainMelGal5.txt.gz 2017-03-21 07:23 6.6M
chainMelGal5Link.sql 2017-03-21 07:23 1.5K
chainMelGal5Link.txt.gz 2017-03-21 07:23 22M
chainNanPar1.sql 2019-02-24 03:22 1.7K
chainNanPar1.txt.gz 2019-02-24 03:22 94M
chainNanPar1Link.sql 2019-02-24 03:22 1.5K
chainNanPar1Link.txt.gz 2019-02-24 03:23 283M
chainRn6.sql 2017-03-28 10:31 1.7K
chainRn6.txt.gz 2017-03-28 10:34 318M
chainRn6Link.sql 2017-03-28 10:44 1.5K
chainRn6Link.txt.gz 2017-03-28 11:06 1.4G
chromAlias.sql 2018-02-18 09:00 1.4K
chromAlias.txt.gz 2018-02-18 09:00 66K
chromInfo.sql 2015-12-21 10:02 1.4K
chromInfo.txt.gz 2015-12-21 10:02 43K
cpgIslandExt.sql 2015-12-21 10:02 1.7K
cpgIslandExt.txt.gz 2015-12-21 10:02 261K
cpgIslandExtUnmasked.sql 2015-12-21 10:02 1.7K
cpgIslandExtUnmasked.txt.gz 2015-12-21 10:02 867K
cytoBandIdeo.sql 2015-12-21 10:02 1.5K
cytoBandIdeo.txt.gz 2015-12-21 10:02 38K
estOrientInfo.sql 2015-12-21 10:02 1.8K
estOrientInfo.txt.gz 2015-12-21 10:02 14M
extNcbiRefSeq.sql 2018-04-08 08:48 1.4K
extNcbiRefSeq.txt.gz 2018-04-08 08:48 91
gap.sql 2015-12-21 10:02 1.6K
gap.txt.gz 2015-12-21 10:02 633K
gbLoaded.sql 2020-09-03 10:12 1.6K
gbLoaded.txt.gz 2020-09-03 10:12 46K
gc5BaseBw.sql 2015-12-21 10:02 1.3K
gc5BaseBw.txt.gz 2015-12-21 10:02 63
genscan.sql 2015-12-21 10:02 1.7K
genscan.txt.gz 2015-12-21 10:02 2.3M
gold.sql 2015-12-21 10:02 1.7K
gold.txt.gz 2015-12-21 10:02 921K
grp.sql 2015-12-21 10:02 1.3K
grp.txt.gz 2015-12-21 10:02 206
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
history.sql 2015-12-21 09:55 1.6K
history.txt.gz 2015-12-21 09:55 937
intronEst.sql 2015-12-21 09:56 2.1K
intronEst.txt.gz 2015-12-21 09:56 33M
mgcFullMrna.sql 2020-03-01 09:24 2.1K
mgcFullMrna.txt.gz 2020-03-01 09:24 904K
mgcGenes.sql 2020-03-01 09:24 1.9K
mgcGenes.txt.gz 2020-03-01 09:24 781K
microsat.sql 2015-12-21 10:02 1.5K
microsat.txt.gz 2015-12-21 10:02 145K
mrnaOrientInfo.sql 2020-09-03 10:12 1.8K
mrnaOrientInfo.txt.gz 2020-09-03 10:12 521K
ncbiRefSeq.sql 2018-04-08 08:48 1.9K
ncbiRefSeq.txt.gz 2018-04-08 08:48 2.9M
ncbiRefSeqCds.sql 2018-04-08 08:48 1.3K
ncbiRefSeqCds.txt.gz 2018-04-08 08:48 277K
ncbiRefSeqCurated.sql 2018-04-08 08:48 2.0K
ncbiRefSeqCurated.txt.gz 2018-04-08 08:48 872K
ncbiRefSeqLink.sql 2018-04-08 08:48 2.0K
ncbiRefSeqLink.txt.gz 2018-04-08 08:48 1.4M
ncbiRefSeqOther.sql 2018-04-08 08:48 1.3K
ncbiRefSeqOther.txt.gz 2018-04-08 08:48 75
ncbiRefSeqPepTable.sql 2018-04-08 08:48 1.4K
ncbiRefSeqPepTable.txt.gz 2018-04-08 08:48 9.6M
ncbiRefSeqPredicted.sql 2018-04-08 08:48 2.0K
ncbiRefSeqPredicted.txt.gz 2018-04-08 08:48 2.3M
ncbiRefSeqPsl.sql 2018-04-08 08:48 2.1K
ncbiRefSeqPsl.txt.gz 2018-04-08 08:48 3.6M
nestedRepeats.sql 2015-12-21 10:02 1.9K
nestedRepeats.txt.gz 2015-12-21 10:02 4.4M
netHg38.sql 2015-12-21 10:02 2.1K
netHg38.txt.gz 2015-12-21 10:02 11M
netMelGal5.sql 2017-03-21 07:24 2.1K
netMelGal5.txt.gz 2017-03-21 07:24 5.5M
netNanPar1.sql 2019-02-24 03:24 2.1K
netNanPar1.txt.gz 2019-02-24 03:24 12M
netRn6.sql 2017-03-28 12:02 2.1K
netRn6.txt.gz 2017-03-28 12:02 12M
refFlat.sql 2020-09-03 10:12 1.7K
refFlat.txt.gz 2020-09-03 10:12 855K
refGene.sql 2020-09-03 10:12 1.9K
refGene.txt.gz 2020-09-03 10:12 913K
refSeqAli.sql 2020-09-03 10:12 2.1K
refSeqAli.txt.gz 2020-09-03 10:12 954K
rmsk.sql 2015-12-21 10:02 1.9K
rmsk.txt.gz 2015-12-21 10:03 57M
seqNcbiRefSeq.sql 2018-04-08 08:48 1.5K
seqNcbiRefSeq.txt.gz 2018-04-08 08:48 667K
simpleRepeat.sql 2015-12-21 10:03 1.9K
simpleRepeat.txt.gz 2015-12-21 10:03 19M
tableDescriptions.sql 2024-11-16 02:04 1.5K
tableDescriptions.txt.gz 2024-11-16 02:04 6.3K
tableList.sql 2024-11-17 03:39 1.6K
tableList.txt.gz 2024-11-17 03:39 3.6K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 34K
ucscToINSDC.sql 2015-12-21 10:03 1.4K
ucscToINSDC.txt.gz 2015-12-21 10:03 56K
ucscToRefSeq.sql 2018-02-18 09:00 1.4K
ucscToRefSeq.txt.gz 2018-02-18 09:00 58K
windowmaskerSdust.sql 2015-12-21 10:03 1.5K
windowmaskerSdust.txt.gz 2015-12-21 10:03 64M
xenoRefFlat.sql 2020-09-03 10:12 1.7K
xenoRefFlat.txt.gz 2020-09-03 10:12 22M
xenoRefGene.sql 2020-09-03 10:12 2.0K
xenoRefGene.txt.gz 2020-09-03 10:12 24M
xenoRefSeqAli.sql 2020-09-03 10:12 2.1K
xenoRefSeqAli.txt.gz 2020-09-03 10:12 21M