This directory contains a dump of the UCSC genome annotation database for the
Mar. 2015 (BGI_ZX_2015/nanPar1) assembly of the tibetan frog genome
(nanPar1, ASM93562v1) .
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/36384
http://www.ncbi.nlm.nih.gov/genome/assembly/302061
http://www.ncbi.nlm.nih.gov/bioproject/243398
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=nanPar1
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/nanPar1/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/nanPar1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nanPar1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nanPar1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nanPar1/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 nanPar1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nanPar1 --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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
augustusGene.sql 2017-04-13 15:41 1.9K
augustusGene.txt.gz 2017-04-13 15:41 2.5M
author.sql 2017-04-13 15:41 1.4K
author.txt.gz 2017-04-13 15:41 3.0M
bigFiles.sql 2024-12-08 03:06 1.4K
bigFiles.txt.gz 2024-12-08 03:06 95
cds.sql 2017-04-13 15:41 1.4K
cds.txt.gz 2017-04-13 15:41 1.9M
cell.sql 2017-04-13 15:41 1.4K
cell.txt.gz 2017-04-13 15:41 40
chainGalGal6.sql 2019-01-20 20:20 1.7K
chainGalGal6.txt.gz 2019-01-20 20:20 16M
chainGalGal6Link.sql 2019-01-20 20:20 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:20 74M
chainXenTro7.sql 2019-08-18 03:19 1.7K
chainXenTro7.txt.gz 2019-08-18 03:20 91M
chainXenTro7Link.sql 2019-08-18 03:20 1.5K
chainXenTro7Link.txt.gz 2019-08-18 03:20 277M
chainXenTro9.sql 2017-12-14 12:42 1.7K
chainXenTro9.txt.gz 2017-12-14 12:42 93M
chainXenTro9Link.sql 2017-12-14 12:43 1.5K
chainXenTro9Link.txt.gz 2017-12-14 12:43 285M
chromAlias.sql 2017-04-13 16:01 1.4K
chromAlias.txt.gz 2017-04-13 16:01 242K
chromInfo.sql 2017-04-13 16:02 1.4K
chromInfo.txt.gz 2017-04-13 16:02 95K
cpgIslandExt.sql 2017-04-13 16:02 1.7K
cpgIslandExt.txt.gz 2017-04-13 16:02 651K
cpgIslandExtUnmasked.sql 2017-04-13 16:02 1.7K
cpgIslandExtUnmasked.txt.gz 2017-04-13 16:02 4.2M
cytoBandIdeo.sql 2017-04-13 16:02 1.5K
cytoBandIdeo.txt.gz 2017-04-13 16:02 88K
description.sql 2017-04-13 16:02 1.4K
description.txt.gz 2017-04-13 16:02 8.4M
development.sql 2017-04-13 16:02 1.4K
development.txt.gz 2017-04-13 16:02 47
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
gap.sql 2017-04-13 16:02 1.6K
gap.txt.gz 2017-04-13 16:02 1.5M
gbCdnaInfo.sql 2017-04-13 16:02 2.6K
gbCdnaInfo.txt.gz 2017-04-13 16:02 7.9M
gbExtFile.sql 2017-04-13 16:03 1.4K
gbExtFile.txt.gz 2017-04-13 16:03 548
gbLoaded.sql 2020-08-19 20:15 1.6K
gbLoaded.txt.gz 2020-08-19 20:15 5.5K
gbMiscDiff.sql 2017-04-13 16:03 1.5K
gbMiscDiff.txt.gz 2017-04-13 16:03 1.5K
gbSeq.sql 2017-04-13 16:03 1.7K
gbSeq.txt.gz 2017-04-13 16:03 12M
gbStatus.sql 2017-04-13 16:04 1.9K
gbStatus.txt.gz 2017-04-13 16:04 3.5M
gbWarn.sql 2017-04-13 16:04 1.3K
gbWarn.txt.gz 2017-04-13 16:04 31
gc5BaseBw.sql 2017-04-13 16:04 1.3K
gc5BaseBw.txt.gz 2017-04-13 16:04 66
geneName.sql 2017-04-13 16:05 1.4K
geneName.txt.gz 2017-04-13 16:05 2.3M
genscan.sql 2017-04-13 15:41 1.7K
genscan.txt.gz 2017-04-13 15:41 2.5M
gold.sql 2017-04-13 15:46 1.7K
gold.txt.gz 2017-04-13 15:46 2.1M
grp.sql 2017-04-13 16:01 1.3K
grp.txt.gz 2017-04-13 16:01 213
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 877
history.sql 2017-04-13 16:02 1.6K
history.txt.gz 2017-04-13 16:02 640
imageClone.sql 2017-04-13 16:02 1.5K
imageClone.txt.gz 2017-04-13 16:02 35
keyword.sql 2017-04-13 16:02 1.4K
keyword.txt.gz 2017-04-13 16:02 460
library.sql 2017-04-13 16:02 1.4K
library.txt.gz 2017-04-13 16:02 43
microsat.sql 2017-04-13 15:41 1.5K
microsat.txt.gz 2017-04-13 15:41 89K
mrnaClone.sql 2017-04-13 15:41 1.4K
mrnaClone.txt.gz 2017-04-13 15:41 1.3K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.0M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 159K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 754K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 6.1M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.0M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.2M
nestedRepeats.sql 2017-04-13 15:41 1.9K
nestedRepeats.txt.gz 2017-04-13 15:41 144K
netGalGal6.sql 2019-01-20 20:20 2.1K
netGalGal6.txt.gz 2019-01-20 20:20 8.7M
netXenTro7.sql 2019-08-18 03:21 2.1K
netXenTro7.txt.gz 2019-08-18 03:21 13M
netXenTro9.sql 2017-12-14 12:44 2.1K
netXenTro9.txt.gz 2017-12-14 12:44 14M
organism.sql 2017-04-13 16:02 1.4K
organism.txt.gz 2017-04-13 16:02 266K
productName.sql 2017-04-13 16:03 1.4K
productName.txt.gz 2017-04-13 16:03 2.7M
refLink.sql 2017-04-13 16:03 1.7K
refLink.txt.gz 2017-04-13 16:03 11M
refSeqStatus.sql 2017-04-13 16:04 1.6K
refSeqStatus.txt.gz 2017-04-13 16:04 1.5M
refSeqSummary.sql 2017-04-13 16:04 1.5K
refSeqSummary.txt.gz 2017-04-13 16:04 5.9M
rmsk.sql 2017-04-13 16:04 1.9K
rmsk.txt.gz 2017-04-13 16:04 12M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 386K
sex.sql 2017-04-13 16:02 1.4K
sex.txt.gz 2017-04-13 16:02 39
simpleRepeat.sql 2017-04-13 16:05 1.9K
simpleRepeat.txt.gz 2017-04-13 16:05 28M
source.sql 2017-04-13 16:07 1.4K
source.txt.gz 2017-04-13 16:07 271K
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 7.6K
tableList.sql 2024-12-08 03:06 1.6K
tableList.txt.gz 2024-12-08 03:06 3.5K
tissue.sql 2017-04-13 16:07 1.4K
tissue.txt.gz 2017-04-13 16:07 59
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 27K
ucscToINSDC.sql 2017-04-13 16:07 1.4K
ucscToINSDC.txt.gz 2017-04-13 16:07 148K
ucscToRefSeq.sql 2017-04-13 16:07 1.4K
ucscToRefSeq.txt.gz 2017-04-13 16:07 149K
windowmaskerSdust.sql 2017-04-13 16:07 1.5K
windowmaskerSdust.txt.gz 2017-04-13 16:08 105M
xenoRefFlat.sql 2020-08-19 20:02 1.7K
xenoRefFlat.txt.gz 2020-08-19 20:02 27M
xenoRefGene.sql 2020-08-19 20:02 2.0K
xenoRefGene.txt.gz 2020-08-19 20:02 30M
xenoRefSeqAli.sql 2020-08-19 20:13 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 20:13 27M