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.
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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 -
chainXenTro9Link.txt.gz 2017-12-14 12:43 285M
chainXenTro7Link.txt.gz 2019-08-18 03:20 277M
windowmaskerSdust.txt.gz 2017-04-13 16:08 105M
chainXenTro9.txt.gz 2017-12-14 12:42 93M
chainXenTro7.txt.gz 2019-08-18 03:20 91M
chainGalGal6Link.txt.gz 2019-01-20 20:20 74M
xenoRefGene.txt.gz 2020-08-19 20:02 30M
simpleRepeat.txt.gz 2017-04-13 16:05 28M
xenoRefSeqAli.txt.gz 2020-08-19 20:13 27M
xenoRefFlat.txt.gz 2020-08-19 20:02 27M
chainGalGal6.txt.gz 2019-01-20 20:20 16M
netXenTro9.txt.gz 2017-12-14 12:44 14M
netXenTro7.txt.gz 2019-08-18 03:21 13M
gbSeq.txt.gz 2017-04-13 16:03 12M
rmsk.txt.gz 2017-04-13 16:04 12M
refLink.txt.gz 2017-04-13 16:03 11M
netGalGal6.txt.gz 2019-01-20 20:20 8.7M
description.txt.gz 2017-04-13 16:02 8.4M
gbCdnaInfo.txt.gz 2017-04-13 16:02 7.9M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 6.1M
refSeqSummary.txt.gz 2017-04-13 16:04 5.9M
cpgIslandExtUnmasked.txt.gz 2017-04-13 16:02 4.2M
gbStatus.txt.gz 2017-04-13 16:04 3.5M
author.txt.gz 2017-04-13 15:41 3.0M
productName.txt.gz 2017-04-13 16:03 2.7M
augustusGene.txt.gz 2017-04-13 15:41 2.5M
genscan.txt.gz 2017-04-13 15:41 2.5M
geneName.txt.gz 2017-04-13 16:05 2.3M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.2M
gold.txt.gz 2017-04-13 15:46 2.1M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.0M
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.0M
cds.txt.gz 2017-04-13 15:41 1.9M
refSeqStatus.txt.gz 2017-04-13 16:04 1.5M
gap.txt.gz 2017-04-13 16:02 1.5M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 754K
cpgIslandExt.txt.gz 2017-04-13 16:02 651K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 386K
source.txt.gz 2017-04-13 16:07 271K
organism.txt.gz 2017-04-13 16:02 266K
chromAlias.txt.gz 2017-04-13 16:01 242K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 159K
ucscToRefSeq.txt.gz 2017-04-13 16:07 149K
ucscToINSDC.txt.gz 2017-04-13 16:07 148K
nestedRepeats.txt.gz 2017-04-13 15:41 144K
chromInfo.txt.gz 2017-04-13 16:02 95K
microsat.txt.gz 2017-04-13 15:41 89K
cytoBandIdeo.txt.gz 2017-04-13 16:02 88K
trackDb.txt.gz 2023-12-05 13:51 27K
tableDescriptions.txt.gz 2024-11-23 02:03 7.6K
gbLoaded.txt.gz 2020-08-19 20:15 5.5K
tableList.txt.gz 2024-11-24 03:06 3.5K
gbCdnaInfo.sql 2017-04-13 16:02 2.6K
xenoRefSeqAli.sql 2020-08-19 20:13 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
netXenTro9.sql 2017-12-14 12:44 2.1K
netXenTro7.sql 2019-08-18 03:21 2.1K
netGalGal6.sql 2019-01-20 20:20 2.1K
trackDb.sql 2023-12-05 13:51 2.1K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
xenoRefGene.sql 2020-08-19 20:02 2.0K
augustusGene.sql 2017-04-13 15:41 1.9K
nestedRepeats.sql 2017-04-13 15:41 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
simpleRepeat.sql 2017-04-13 16:05 1.9K
gbStatus.sql 2017-04-13 16:04 1.9K
rmsk.sql 2017-04-13 16:04 1.9K
hgFindSpec.sql 2023-12-05 13:51 1.8K
xenoRefFlat.sql 2020-08-19 20:02 1.7K
refLink.sql 2017-04-13 16:03 1.7K
cpgIslandExtUnmasked.sql 2017-04-13 16:02 1.7K
chainXenTro9.sql 2017-12-14 12:42 1.7K
chainXenTro7.sql 2019-08-18 03:19 1.7K
chainGalGal6.sql 2019-01-20 20:20 1.7K
gbSeq.sql 2017-04-13 16:03 1.7K
cpgIslandExt.sql 2017-04-13 16:02 1.7K
genscan.sql 2017-04-13 15:41 1.7K
gold.sql 2017-04-13 15:46 1.7K
gbLoaded.sql 2020-08-19 20:15 1.6K
refSeqStatus.sql 2017-04-13 16:04 1.6K
gap.sql 2017-04-13 16:02 1.6K
history.sql 2017-04-13 16:02 1.6K
tableList.sql 2024-11-24 03:06 1.6K
chainXenTro9Link.sql 2017-12-14 12:43 1.5K
chainXenTro7Link.sql 2019-08-18 03:20 1.5K
chainGalGal6Link.sql 2019-01-20 20:20 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
cytoBandIdeo.sql 2017-04-13 16:02 1.5K
windowmaskerSdust.sql 2017-04-13 16:07 1.5K
imageClone.sql 2017-04-13 16:02 1.5K
refSeqSummary.sql 2017-04-13 16:04 1.5K
microsat.sql 2017-04-13 15:41 1.5K
gbMiscDiff.sql 2017-04-13 16:03 1.5K
gbMiscDiff.txt.gz 2017-04-13 16:03 1.5K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ucscToRefSeq.sql 2017-04-13 16:07 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ucscToINSDC.sql 2017-04-13 16:07 1.4K
chromAlias.sql 2017-04-13 16:01 1.4K
productName.sql 2017-04-13 16:03 1.4K
development.sql 2017-04-13 16:02 1.4K
description.sql 2017-04-13 16:02 1.4K
mrnaClone.sql 2017-04-13 15:41 1.4K
organism.sql 2017-04-13 16:02 1.4K
geneName.sql 2017-04-13 16:05 1.4K
library.sql 2017-04-13 16:02 1.4K
keyword.sql 2017-04-13 16:02 1.4K
gbExtFile.sql 2017-04-13 16:03 1.4K
tissue.sql 2017-04-13 16:07 1.4K
source.sql 2017-04-13 16:07 1.4K
author.sql 2017-04-13 15:41 1.4K
cell.sql 2017-04-13 15:41 1.4K
sex.sql 2017-04-13 16:02 1.4K
cds.sql 2017-04-13 15:41 1.4K
chromInfo.sql 2017-04-13 16:02 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
grp.sql 2017-04-13 16:01 1.3K
mrnaClone.txt.gz 2017-04-13 15:41 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
gbWarn.sql 2017-04-13 16:04 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
gc5BaseBw.sql 2017-04-13 16:04 1.3K
hgFindSpec.txt.gz 2023-12-05 13:51 877
history.txt.gz 2017-04-13 16:02 640
gbExtFile.txt.gz 2017-04-13 16:03 548
keyword.txt.gz 2017-04-13 16:02 460
grp.txt.gz 2017-04-13 16:01 213
bigFiles.txt.gz 2024-11-24 03:06 95
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
gc5BaseBw.txt.gz 2017-04-13 16:04 66
tissue.txt.gz 2017-04-13 16:07 59
development.txt.gz 2017-04-13 16:02 47
library.txt.gz 2017-04-13 16:02 43
cell.txt.gz 2017-04-13 15:41 40
sex.txt.gz 2017-04-13 16:02 39
imageClone.txt.gz 2017-04-13 16:02 35
gbWarn.txt.gz 2017-04-13 16:04 31