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.
---------------------------------------------------------------
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.
-----------------------------------------------------------------------------
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 -
chainRn6Link.txt.gz 2017-03-28 11:06 1.4G
chainHg38Link.txt.gz 2015-12-21 09:58 1.0G
chainRn6.txt.gz 2017-03-28 10:34 318M
chainNanPar1Link.txt.gz 2019-02-24 03:23 283M
chainHg38.txt.gz 2015-12-21 09:56 229M
chainNanPar1.txt.gz 2019-02-24 03:22 94M
windowmaskerSdust.txt.gz 2015-12-21 10:03 64M
rmsk.txt.gz 2015-12-21 10:03 57M
all_est.txt.gz 2015-12-21 09:55 52M
intronEst.txt.gz 2015-12-21 09:56 33M
xenoRefGene.txt.gz 2020-09-03 10:12 24M
chainMelGal5Link.txt.gz 2017-03-21 07:23 22M
xenoRefFlat.txt.gz 2020-09-03 10:12 22M
xenoRefSeqAli.txt.gz 2020-09-03 10:12 21M
simpleRepeat.txt.gz 2015-12-21 10:03 19M
estOrientInfo.txt.gz 2015-12-21 10:02 14M
netNanPar1.txt.gz 2019-02-24 03:24 12M
netRn6.txt.gz 2017-03-28 12:02 12M
netHg38.txt.gz 2015-12-21 10:02 11M
ncbiRefSeqPepTable.txt.gz 2018-04-08 08:48 9.6M
chainMelGal5.txt.gz 2017-03-21 07:23 6.6M
netMelGal5.txt.gz 2017-03-21 07:24 5.5M
nestedRepeats.txt.gz 2015-12-21 10:02 4.4M
ncbiRefSeqPsl.txt.gz 2018-04-08 08:48 3.6M
ncbiRefSeq.txt.gz 2018-04-08 08:48 2.9M
genscan.txt.gz 2015-12-21 10:02 2.3M
ncbiRefSeqPredicted.txt.gz 2018-04-08 08:48 2.3M
augustusGene.txt.gz 2015-12-21 09:56 2.2M
all_mrna.txt.gz 2020-05-11 17:36 1.9M
ncbiRefSeqLink.txt.gz 2018-04-08 08:48 1.4M
refSeqAli.txt.gz 2020-09-03 10:12 954K
gold.txt.gz 2015-12-21 10:02 921K
refGene.txt.gz 2020-09-03 10:12 913K
mgcFullMrna.txt.gz 2020-03-01 09:24 904K
ncbiRefSeqCurated.txt.gz 2018-04-08 08:48 872K
cpgIslandExtUnmasked.txt.gz 2015-12-21 10:02 867K
refFlat.txt.gz 2020-09-03 10:12 855K
mgcGenes.txt.gz 2020-03-01 09:24 781K
seqNcbiRefSeq.txt.gz 2018-04-08 08:48 667K
gap.txt.gz 2015-12-21 10:02 633K
mrnaOrientInfo.txt.gz 2020-09-03 10:12 521K
ncbiRefSeqCds.txt.gz 2018-04-08 08:48 277K
cpgIslandExt.txt.gz 2015-12-21 10:02 261K
microsat.txt.gz 2015-12-21 10:02 145K
chromAlias.txt.gz 2018-02-18 09:00 66K
ucscToRefSeq.txt.gz 2018-02-18 09:00 58K
ucscToINSDC.txt.gz 2015-12-21 10:03 56K
gbLoaded.txt.gz 2020-09-03 10:12 46K
chromInfo.txt.gz 2015-12-21 10:02 43K
cytoBandIdeo.txt.gz 2015-12-21 10:02 38K
trackDb.txt.gz 2023-12-05 13:52 34K
tableDescriptions.txt.gz 2024-11-23 02:04 6.3K
tableList.txt.gz 2024-11-24 03:27 3.6K
xenoRefSeqAli.sql 2020-09-03 10:12 2.1K
refSeqAli.sql 2020-09-03 10:12 2.1K
all_mrna.sql 2020-05-11 17:36 2.1K
ncbiRefSeqPsl.sql 2018-04-08 08:48 2.1K
mgcFullMrna.sql 2020-03-01 09:24 2.1K
intronEst.sql 2015-12-21 09:56 2.1K
all_est.sql 2015-12-21 09:55 2.1K
netNanPar1.sql 2019-02-24 03:24 2.1K
netMelGal5.sql 2017-03-21 07:24 2.1K
netHg38.sql 2015-12-21 10:02 2.1K
netRn6.sql 2017-03-28 12:02 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2018-04-08 08:48 2.0K
ncbiRefSeqPredicted.sql 2018-04-08 08:48 2.0K
xenoRefGene.sql 2020-09-03 10:12 2.0K
ncbiRefSeqCurated.sql 2018-04-08 08:48 2.0K
refGene.sql 2020-09-03 10:12 1.9K
augustusGene.sql 2015-12-21 09:56 1.9K
nestedRepeats.sql 2015-12-21 10:02 1.9K
ncbiRefSeq.sql 2018-04-08 08:48 1.9K
simpleRepeat.sql 2015-12-21 10:03 1.9K
mgcGenes.sql 2020-03-01 09:24 1.9K
rmsk.sql 2015-12-21 10:02 1.9K
mrnaOrientInfo.sql 2020-09-03 10:12 1.8K
estOrientInfo.sql 2015-12-21 10:02 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-09-03 10:12 1.7K
refFlat.sql 2020-09-03 10:12 1.7K
cpgIslandExtUnmasked.sql 2015-12-21 10:02 1.7K
chainNanPar1.sql 2019-02-24 03:22 1.7K
chainMelGal5.sql 2017-03-21 07:23 1.7K
chainHg38.sql 2015-12-21 09:56 1.7K
chainRn6.sql 2017-03-28 10:31 1.7K
cpgIslandExt.sql 2015-12-21 10:02 1.7K
genscan.sql 2015-12-21 10:02 1.7K
gold.sql 2015-12-21 10:02 1.7K
gbLoaded.sql 2020-09-03 10:12 1.6K
gap.sql 2015-12-21 10:02 1.6K
history.sql 2015-12-21 09:55 1.6K
tableList.sql 2024-11-24 03:27 1.6K
seqNcbiRefSeq.sql 2018-04-08 08:48 1.5K
chainNanPar1Link.sql 2019-02-24 03:22 1.5K
chainMelGal5Link.sql 2017-03-21 07:23 1.5K
chainHg38Link.sql 2015-12-21 09:57 1.5K
chainRn6Link.sql 2017-03-28 10:44 1.5K
cytoBandIdeo.sql 2015-12-21 10:02 1.5K
windowmaskerSdust.sql 2015-12-21 10:03 1.5K
microsat.sql 2015-12-21 10:02 1.5K
extNcbiRefSeq.sql 2018-04-08 08:48 1.4K
ucscToRefSeq.sql 2018-02-18 09:00 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
ucscToINSDC.sql 2015-12-21 10:03 1.4K
chromAlias.sql 2018-02-18 09:00 1.4K
chromInfo.sql 2015-12-21 10:02 1.4K
bigFiles.sql 2024-11-24 03:27 1.4K
ncbiRefSeqPepTable.sql 2018-04-08 08:48 1.4K
grp.sql 2015-12-21 10:02 1.3K
ncbiRefSeqCds.sql 2018-04-08 08:48 1.3K
ncbiRefSeqOther.sql 2018-04-08 08:48 1.3K
gc5BaseBw.sql 2015-12-21 10:02 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
history.txt.gz 2015-12-21 09:55 937
grp.txt.gz 2015-12-21 10:02 206
bigFiles.txt.gz 2024-11-24 03:27 94
extNcbiRefSeq.txt.gz 2018-04-08 08:48 91
ncbiRefSeqOther.txt.gz 2018-04-08 08:48 75
gc5BaseBw.txt.gz 2015-12-21 10:02 63