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 -
gc5BaseBw.txt.gz 21-Dec-2015 10:02 63
bigFiles.txt.gz 23-Jul-2017 04:39 68
grp.txt.gz 21-Dec-2015 10:02 206
hgFindSpec_public.txt.gz 02-Jan-2017 05:45 638
hgFindSpec.txt.gz 23-Jul-2017 04:39 639
history.txt.gz 21-Dec-2015 09:55 937
gc5BaseBw.sql 21-Dec-2015 10:02 1.3K
grp.sql 21-Dec-2015 10:02 1.3K
bigFiles.sql 23-Jul-2017 04:39 1.4K
chromInfo.sql 21-Dec-2015 10:02 1.4K
tableDescriptions.sql 23-Jul-2017 04:39 1.4K
ucscToINSDC.sql 21-Dec-2015 10:03 1.4K
microsat.sql 21-Dec-2015 10:02 1.5K
windowmaskerSdust.sql 21-Dec-2015 10:03 1.5K
cytoBandIdeo.sql 21-Dec-2015 10:02 1.5K
chainRn6Link.sql 28-Mar-2017 10:44 1.5K
chainHg38Link.sql 21-Dec-2015 09:57 1.5K
tableList.sql 23-Jul-2017 04:39 1.5K
chainMelGal5Link.sql 21-Mar-2017 07:23 1.5K
history.sql 21-Dec-2015 09:55 1.6K
gbLoaded.sql 09-Jul-2017 13:22 1.6K
gap.sql 21-Dec-2015 10:02 1.6K
gold.sql 21-Dec-2015 10:02 1.7K
genscan.sql 21-Dec-2015 10:02 1.7K
cpgIslandExt.sql 21-Dec-2015 10:02 1.7K
chainRn6.sql 28-Mar-2017 10:31 1.7K
chainHg38.sql 21-Dec-2015 09:56 1.7K
refFlat.sql 09-Jul-2017 13:22 1.7K
chainMelGal5.sql 21-Mar-2017 07:23 1.7K
cpgIslandExtUnmasked.sql 21-Dec-2015 10:02 1.7K
xenoRefFlat.sql 09-Jul-2017 13:22 1.7K
hgFindSpec.sql 23-Jul-2017 04:39 1.7K
hgFindSpec_public.sql 02-Jan-2017 05:45 1.8K
estOrientInfo.sql 21-Dec-2015 10:02 1.8K
mrnaOrientInfo.sql 09-Jul-2017 13:22 1.8K
rmsk.sql 21-Dec-2015 10:02 1.9K
refGene.sql 09-Jul-2017 13:22 1.9K
mgcGenes.sql 13-Jun-2017 20:11 1.9K
simpleRepeat.sql 21-Dec-2015 10:03 1.9K
nestedRepeats.sql 21-Dec-2015 10:02 1.9K
xenoRefGene.sql 09-Jul-2017 13:22 1.9K
augustusGene.sql 21-Dec-2015 09:56 1.9K
trackDb.sql 23-Jul-2017 04:39 2.0K
trackDb_public.sql 02-Jan-2017 05:44 2.1K
netRn6.sql 28-Mar-2017 12:02 2.1K
netHg38.sql 21-Dec-2015 10:02 2.1K
netMelGal5.sql 21-Mar-2017 07:24 2.1K
all_est.sql 21-Dec-2015 09:55 2.1K
all_mrna.sql 25-Jun-2017 22:37 2.1K
intronEst.sql 21-Dec-2015 09:56 2.1K
refSeqAli.sql 09-Jul-2017 13:22 2.1K
mgcFullMrna.sql 13-Jun-2017 20:11 2.1K
xenoRefSeqAli.sql 09-Jul-2017 13:23 2.1K
tableList.txt.gz 23-Jul-2017 04:39 3.0K
tableDescriptions.txt.gz 23-Jul-2017 04:39 4.3K
gbLoaded.txt.gz 09-Jul-2017 13:22 19K
trackDb_public.txt.gz 02-Jan-2017 05:44 20K
trackDb.txt.gz 23-Jul-2017 04:39 30K
cytoBandIdeo.txt.gz 21-Dec-2015 10:02 38K
chromInfo.txt.gz 21-Dec-2015 10:02 43K
ucscToINSDC.txt.gz 21-Dec-2015 10:03 56K
microsat.txt.gz 21-Dec-2015 10:02 145K
cpgIslandExt.txt.gz 21-Dec-2015 10:02 261K
mrnaOrientInfo.txt.gz 09-Jul-2017 13:22 457K
gap.txt.gz 21-Dec-2015 10:02 633K
mgcGenes.txt.gz 13-Jun-2017 20:11 833K
refFlat.txt.gz 09-Jul-2017 13:22 844K
cpgIslandExtUnmasked.txt.gz 21-Dec-2015 10:02 867K
refGene.txt.gz 09-Jul-2017 13:22 903K
mgcFullMrna.txt.gz 13-Jun-2017 20:11 908K
gold.txt.gz 21-Dec-2015 10:02 921K
refSeqAli.txt.gz 09-Jul-2017 13:22 942K
all_mrna.txt.gz 25-Jun-2017 22:37 1.6M
augustusGene.txt.gz 21-Dec-2015 09:56 2.2M
genscan.txt.gz 21-Dec-2015 10:02 2.3M
nestedRepeats.txt.gz 21-Dec-2015 10:02 4.4M
netMelGal5.txt.gz 21-Mar-2017 07:24 5.5M
chainMelGal5.txt.gz 21-Mar-2017 07:23 6.6M
netHg38.txt.gz 21-Dec-2015 10:02 11M
netRn6.txt.gz 28-Mar-2017 12:02 12M
estOrientInfo.txt.gz 21-Dec-2015 10:02 14M
xenoRefSeqAli.txt.gz 09-Jul-2017 13:23 17M
xenoRefFlat.txt.gz 09-Jul-2017 13:22 19M
simpleRepeat.txt.gz 21-Dec-2015 10:03 19M
xenoRefGene.txt.gz 09-Jul-2017 13:22 21M
chainMelGal5Link.txt.gz 21-Mar-2017 07:23 22M
intronEst.txt.gz 21-Dec-2015 09:56 33M
all_est.txt.gz 21-Dec-2015 09:55 52M
rmsk.txt.gz 21-Dec-2015 10:03 57M
windowmaskerSdust.txt.gz 21-Dec-2015 10:03 64M
chainHg38.txt.gz 21-Dec-2015 09:56 229M
chainRn6.txt.gz 28-Mar-2017 10:34 318M
chainHg38Link.txt.gz 21-Dec-2015 09:58 1.0G
chainRn6Link.txt.gz 28-Mar-2017 11:06 1.4G