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