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 -
gc5BaseBw.txt.gz 2021-02-22 12:16 67
crisprAllTargets.txt.gz 2021-02-25 03:01 70
ncbiRefSeqOther.txt.gz 2021-02-22 22:04 76
extNcbiRefSeq.txt.gz 2021-02-22 22:04 92
bigFiles.txt.gz 2024-11-17 03:13 120
grp.txt.gz 2021-02-22 12:16 213
history.txt.gz 2021-03-31 14:18 1.0K
cytoBandIdeo.txt.gz 2021-02-22 12:39 1.0K
chromInfo.txt.gz 2021-02-22 12:16 1.1K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
gc5BaseBw.sql 2021-02-22 12:16 1.3K
ncbiRefSeqOther.sql 2021-02-22 22:04 1.3K
crisprAllTargets.sql 2021-02-25 03:01 1.3K
gbLoaded.txt.gz 2021-03-25 15:56 1.3K
ncbiRefSeqCds.sql 2021-02-22 22:04 1.4K
grp.sql 2021-02-22 12:16 1.4K
ncbiRefSeqPepTable.sql 2021-03-31 14:18 1.4K
bigFiles.sql 2024-11-17 03:13 1.4K
chromInfo.sql 2021-02-22 12:16 1.4K
ucscToRefSeq.txt.gz 2021-02-22 13:28 1.4K
ucscToINSDC.txt.gz 2021-02-22 13:28 1.4K
chromAlias.sql 2021-02-22 13:19 1.4K
ucscToINSDC.sql 2021-02-22 13:28 1.4K
ucscToRefSeq.sql 2021-02-22 13:28 1.5K
tableDescriptions.sql 2024-11-16 02:04 1.5K
extNcbiRefSeq.sql 2021-02-22 22:04 1.5K
microsat.sql 2021-02-22 16:05 1.5K
windowmaskerSdust.sql 2021-02-22 16:52 1.5K
cytoBandIdeo.sql 2021-02-22 12:39 1.5K
chainHg38Link.sql 2021-02-23 12:30 1.6K
chainMm10Link.sql 2021-02-23 07:59 1.6K
chainMm39Link.sql 2021-02-23 07:47 1.6K
seqNcbiRefSeq.sql 2021-02-22 22:04 1.6K
tableList.sql 2024-11-17 03:13 1.6K
history.sql 2021-03-31 14:18 1.6K
gbLoaded.sql 2021-03-25 15:56 1.6K
gap.sql 2021-02-22 12:15 1.6K
gold.sql 2021-02-22 12:15 1.7K
genscan.sql 2021-02-23 11:30 1.7K
cpgIslandExt.sql 2021-02-22 21:35 1.7K
chainHg38.sql 2021-02-23 12:03 1.7K
chainMm10.sql 2021-02-23 07:54 1.7K
chainMm39.sql 2021-02-23 07:45 1.7K
refFlat.sql 2021-03-24 15:45 1.7K
cpgIslandExtUnmasked.sql 2021-02-22 12:36 1.7K
xenoRefFlat.sql 2021-03-24 15:45 1.7K
hgFindSpec.sql 2023-12-05 13:52 1.8K
estOrientInfo.sql 2021-03-25 15:56 1.8K
mrnaOrientInfo.sql 2021-03-25 15:56 1.8K
rmsk.sql 2021-02-22 18:31 1.9K
refGene.sql 2021-03-24 15:45 1.9K
simpleRepeat.sql 2021-02-22 14:42 1.9K
ncbiRefSeq.sql 2021-02-22 21:40 2.0K
nestedRepeats.sql 2021-02-22 18:32 2.0K
xenoRefGene.sql 2021-03-24 15:45 2.0K
augustusGene.sql 2021-02-22 22:24 2.0K
ncbiRefSeqCurated.sql 2021-02-22 21:40 2.0K
ncbiRefSeqPredicted.sql 2021-02-22 21:40 2.0K
ncbiRefSeqLink.sql 2021-03-31 11:37 2.0K
trackDb.sql 2023-12-05 13:52 2.1K
netHg38.sql 2021-02-23 12:32 2.1K
netMm10.sql 2021-02-23 08:00 2.1K
netMm39.sql 2021-02-23 07:49 2.1K
all_est.sql 2021-03-25 15:56 2.1K
all_mrna.sql 2021-03-24 15:19 2.1K
intronEst.sql 2021-03-25 15:56 2.1K
refSeqAli.sql 2021-03-24 15:45 2.1K
ncbiRefSeqPsl.sql 2021-02-22 21:40 2.1K
xenoRefSeqAli.sql 2021-03-24 15:45 2.1K
chromAlias.txt.gz 2021-02-22 13:19 2.6K
tableList.txt.gz 2024-11-17 03:13 3.2K
tableDescriptions.txt.gz 2024-11-16 02:04 6.2K
gap.txt.gz 2021-02-22 12:15 10K
gold.txt.gz 2021-02-22 12:15 16K
trackDb.txt.gz 2023-12-05 13:52 31K
microsat.txt.gz 2021-02-22 16:05 156K
ncbiRefSeqCds.txt.gz 2021-02-22 22:04 313K
cpgIslandExt.txt.gz 2021-02-22 21:35 342K
mrnaOrientInfo.txt.gz 2021-03-25 15:56 510K
seqNcbiRefSeq.txt.gz 2021-02-22 22:04 759K
refFlat.txt.gz 2021-03-24 15:45 848K
ncbiRefSeqCurated.txt.gz 2021-02-22 21:40 924K
refGene.txt.gz 2021-03-24 15:45 928K
refSeqAli.txt.gz 2021-03-24 15:45 961K
cpgIslandExtUnmasked.txt.gz 2021-02-22 12:36 1.1M
ncbiRefSeqLink.txt.gz 2021-03-31 11:37 1.8M
all_mrna.txt.gz 2021-03-24 15:19 1.8M
augustusGene.txt.gz 2021-02-22 22:24 2.3M
genscan.txt.gz 2021-02-23 11:30 2.4M
ncbiRefSeqPredicted.txt.gz 2021-02-22 21:40 2.6M
ncbiRefSeq.txt.gz 2021-02-22 21:40 3.2M
ncbiRefSeqPsl.txt.gz 2021-02-22 21:40 4.1M
nestedRepeats.txt.gz 2021-02-22 18:32 5.1M
xenoRefFlat.txt.gz 2021-03-24 15:45 6.0M
xenoRefGene.txt.gz 2021-03-24 15:45 6.7M
netMm39.txt.gz 2021-02-23 07:49 8.2M
ncbiRefSeqPepTable.txt.gz 2021-03-31 14:18 11M
xenoRefSeqAli.txt.gz 2021-03-24 15:45 11M
netMm10.txt.gz 2021-02-23 08:00 12M
estOrientInfo.txt.gz 2021-03-25 15:56 15M
netHg38.txt.gz 2021-02-23 12:32 15M
simpleRepeat.txt.gz 2021-02-22 14:42 22M
intronEst.txt.gz 2021-03-25 15:56 33M
all_est.txt.gz 2021-03-25 15:56 53M
chainMm39.txt.gz 2021-02-23 07:45 59M
rmsk.txt.gz 2021-02-22 18:31 61M
windowmaskerSdust.txt.gz 2021-02-22 16:52 62M
chainMm10.txt.gz 2021-02-23 07:54 111M
chainMm39Link.txt.gz 2021-02-23 07:47 270M
chainHg38.txt.gz 2021-02-23 12:03 435M
chainMm10Link.txt.gz 2021-02-23 07:59 619M
chainHg38Link.txt.gz 2021-02-23 12:30 2.4G