This directory contains a dump of the UCSC genome annotation database for the
Nov. 2019 (UCB_Xtro_10.0/xenTro10) assembly of the X. tropicalis genome
(xenTro10, University of California, Berkeley)
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:
https://www.ncbi.nlm.nih.gov/genome/80
https://www.ncbi.nlm.nih.gov/genome/assembly/5323661
https://www.ncbi.nlm.nih.gov/bioproject/577946
https://www.ncbi.nlm.nih.gov/biosample/SAMN13041969
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=xenTro10
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/xenTro10/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/xenTro10/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/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 xenTro10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql xenTro10 --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.
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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 2021-03-24 15:45 11M
xenoRefSeqAli.sql 2021-03-24 15:45 2.1K
xenoRefGene.txt.gz 2021-03-24 15:45 6.7M
xenoRefGene.sql 2021-03-24 15:45 2.0K
xenoRefFlat.txt.gz 2021-03-24 15:45 6.0M
xenoRefFlat.sql 2021-03-24 15:45 1.7K
windowmaskerSdust.txt.gz 2021-02-22 16:52 62M
windowmaskerSdust.sql 2021-02-22 16:52 1.5K
ucscToRefSeq.txt.gz 2021-02-22 13:28 1.4K
ucscToRefSeq.sql 2021-02-22 13:28 1.5K
ucscToINSDC.txt.gz 2021-02-22 13:28 1.4K
ucscToINSDC.sql 2021-02-22 13:28 1.4K
trackDb.txt.gz 2023-12-05 13:52 31K
trackDb.sql 2023-12-05 13:52 2.1K
tableList.txt.gz 2024-11-24 03:04 3.2K
tableList.sql 2024-11-24 03:04 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.2K
tableDescriptions.sql 2024-11-23 02:04 1.4K
simpleRepeat.txt.gz 2021-02-22 14:42 22M
simpleRepeat.sql 2021-02-22 14:42 1.9K
seqNcbiRefSeq.txt.gz 2021-02-22 22:04 759K
seqNcbiRefSeq.sql 2021-02-22 22:04 1.6K
rmsk.txt.gz 2021-02-22 18:31 61M
rmsk.sql 2021-02-22 18:31 1.9K
refSeqAli.txt.gz 2021-03-24 15:45 961K
refSeqAli.sql 2021-03-24 15:45 2.1K
refGene.txt.gz 2021-03-24 15:45 928K
refGene.sql 2021-03-24 15:45 1.9K
refFlat.txt.gz 2021-03-24 15:45 848K
refFlat.sql 2021-03-24 15:45 1.7K
netMm39.txt.gz 2021-02-23 07:49 8.2M
netMm39.sql 2021-02-23 07:49 2.1K
netMm10.txt.gz 2021-02-23 08:00 12M
netMm10.sql 2021-02-23 08:00 2.1K
netHg38.txt.gz 2021-02-23 12:32 15M
netHg38.sql 2021-02-23 12:32 2.1K
nestedRepeats.txt.gz 2021-02-22 18:32 5.1M
nestedRepeats.sql 2021-02-22 18:32 2.0K
ncbiRefSeqPsl.txt.gz 2021-02-22 21:40 4.1M
ncbiRefSeqPsl.sql 2021-02-22 21:40 2.1K
ncbiRefSeqPredicted.txt.gz 2021-02-22 21:40 2.6M
ncbiRefSeqPredicted.sql 2021-02-22 21:40 2.0K
ncbiRefSeqPepTable.txt.gz 2021-03-31 14:18 11M
ncbiRefSeqPepTable.sql 2021-03-31 14:18 1.4K
ncbiRefSeqOther.txt.gz 2021-02-22 22:04 76
ncbiRefSeqOther.sql 2021-02-22 22:04 1.3K
ncbiRefSeqLink.txt.gz 2021-03-31 11:37 1.8M
ncbiRefSeqLink.sql 2021-03-31 11:37 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-22 21:40 924K
ncbiRefSeqCurated.sql 2021-02-22 21:40 2.0K
ncbiRefSeqCds.txt.gz 2021-02-22 22:04 313K
ncbiRefSeqCds.sql 2021-02-22 22:04 1.4K
ncbiRefSeq.txt.gz 2021-02-22 21:40 3.2M
ncbiRefSeq.sql 2021-02-22 21:40 2.0K
mrnaOrientInfo.txt.gz 2021-03-25 15:56 510K
mrnaOrientInfo.sql 2021-03-25 15:56 1.8K
microsat.txt.gz 2021-02-22 16:05 156K
microsat.sql 2021-02-22 16:05 1.5K
intronEst.txt.gz 2021-03-25 15:56 33M
intronEst.sql 2021-03-25 15:56 2.1K
history.txt.gz 2021-03-31 14:18 1.0K
history.sql 2021-03-31 14:18 1.6K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
hgFindSpec.sql 2023-12-05 13:52 1.8K
grp.txt.gz 2021-02-22 12:16 213
grp.sql 2021-02-22 12:16 1.4K
gold.txt.gz 2021-02-22 12:15 16K
gold.sql 2021-02-22 12:15 1.7K
genscan.txt.gz 2021-02-23 11:30 2.4M
genscan.sql 2021-02-23 11:30 1.7K
gc5BaseBw.txt.gz 2021-02-22 12:16 67
gc5BaseBw.sql 2021-02-22 12:16 1.3K
gbLoaded.txt.gz 2021-03-25 15:56 1.3K
gbLoaded.sql 2021-03-25 15:56 1.6K
gap.txt.gz 2021-02-22 12:15 10K
gap.sql 2021-02-22 12:15 1.6K
extNcbiRefSeq.txt.gz 2021-02-22 22:04 92
extNcbiRefSeq.sql 2021-02-22 22:04 1.5K
estOrientInfo.txt.gz 2021-03-25 15:56 15M
estOrientInfo.sql 2021-03-25 15:56 1.8K
cytoBandIdeo.txt.gz 2021-02-22 12:39 1.0K
cytoBandIdeo.sql 2021-02-22 12:39 1.5K
crisprAllTargets.txt.gz 2021-02-25 03:01 70
crisprAllTargets.sql 2021-02-25 03:01 1.3K
cpgIslandExtUnmasked.txt.gz 2021-02-22 12:36 1.1M
cpgIslandExtUnmasked.sql 2021-02-22 12:36 1.7K
cpgIslandExt.txt.gz 2021-02-22 21:35 342K
cpgIslandExt.sql 2021-02-22 21:35 1.7K
chromInfo.txt.gz 2021-02-22 12:16 1.1K
chromInfo.sql 2021-02-22 12:16 1.4K
chromAlias.txt.gz 2021-02-22 13:19 2.6K
chromAlias.sql 2021-02-22 13:19 1.4K
chainMm39Link.txt.gz 2021-02-23 07:47 270M
chainMm39Link.sql 2021-02-23 07:47 1.6K
chainMm39.txt.gz 2021-02-23 07:45 59M
chainMm39.sql 2021-02-23 07:45 1.7K
chainMm10Link.txt.gz 2021-02-23 07:59 619M
chainMm10Link.sql 2021-02-23 07:59 1.6K
chainMm10.txt.gz 2021-02-23 07:54 111M
chainMm10.sql 2021-02-23 07:54 1.7K
chainHg38Link.txt.gz 2021-02-23 12:30 2.4G
chainHg38Link.sql 2021-02-23 12:30 1.6K
chainHg38.txt.gz 2021-02-23 12:03 435M
chainHg38.sql 2021-02-23 12:03 1.7K
bigFiles.txt.gz 2024-11-24 03:04 120
bigFiles.sql 2024-11-24 03:04 1.4K
augustusGene.txt.gz 2021-02-22 22:24 2.3M
augustusGene.sql 2021-02-22 22:24 2.0K
all_mrna.txt.gz 2021-03-24 15:19 1.8M
all_mrna.sql 2021-03-24 15:19 2.1K
all_est.txt.gz 2021-03-25 15:56 53M
all_est.sql 2021-03-25 15:56 2.1K