This directory contains a dump of the UCSC genome annotation database for the
Aug 2014 (M_pentadactyla-1.1.1/manPen1) assembly of the chinese pangolin genome
(manPen1, Washington University (WashU) GCA_000738955.1) .
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/10694
http://www.ncbi.nlm.nih.gov/genome/assembly/203041
http://www.ncbi.nlm.nih.gov/bioproject/20331
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=manPen1
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/manPen1/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/manPen1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/manPen1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/manPen1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/manPen1/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 manPen1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql manPen1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Chinese pangolin sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
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 these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. 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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
augustusGene.sql 2017-04-21 09:35 1.9K
augustusGene.txt.gz 2017-04-21 09:35 1.9M
gbWarn.sql 2017-04-21 09:35 1.3K
gbWarn.txt.gz 2017-04-21 09:35 31
keyword.sql 2017-04-21 09:35 1.4K
keyword.txt.gz 2017-04-21 09:35 778
library.sql 2017-04-21 09:35 1.4K
library.txt.gz 2017-04-21 09:35 43
microsat.sql 2017-04-21 09:35 1.5K
microsat.txt.gz 2017-04-21 09:35 221K
cell.sql 2017-04-21 09:35 1.4K
cell.txt.gz 2017-04-21 09:35 40
chainHg38.sql 2017-04-21 09:35 1.7K
mrnaClone.sql 2017-04-21 09:35 1.4K
mrnaClone.txt.gz 2017-04-21 09:35 1.4K
chainHg38.txt.gz 2017-04-21 09:38 203M
chainHg38Link.sql 2017-04-21 09:46 1.5K
chainHg38Link.txt.gz 2017-04-21 09:55 834M
gc5BaseBw.sql 2017-04-21 10:23 1.3K
gc5BaseBw.txt.gz 2017-04-21 10:23 66
nestedRepeats.sql 2017-04-21 10:23 1.9K
nestedRepeats.txt.gz 2017-04-21 10:23 7.6M
chainMm10.sql 2017-04-21 10:23 1.7K
chainMm10.txt.gz 2017-04-21 10:24 54M
chainMm10Link.sql 2017-04-21 10:26 1.5K
chainMm10Link.txt.gz 2017-04-21 10:31 441M
chromAlias.sql 2017-04-21 10:48 1.4K
chromAlias.txt.gz 2017-04-21 10:48 449K
genscan.sql 2017-04-21 10:48 1.7K
genscan.txt.gz 2017-04-21 10:48 2.8M
netHg38.sql 2017-04-21 10:48 2.1K
netHg38.txt.gz 2017-04-21 10:49 44M
chromInfo.sql 2017-04-21 10:51 1.4K
chromInfo.txt.gz 2017-04-21 10:51 365K
cpgIslandExt.sql 2017-04-21 10:51 1.7K
cpgIslandExt.txt.gz 2017-04-21 10:51 564K
gold.sql 2017-04-21 10:51 1.7K
gold.txt.gz 2017-04-21 10:51 2.7M
rmsk.sql 2017-04-21 10:51 1.9K
rmsk.txt.gz 2017-04-21 10:52 67M
cpgIslandExtUnmasked.sql 2017-04-21 10:54 1.7K
cpgIslandExtUnmasked.txt.gz 2017-04-21 10:54 612K
cytoBandIdeo.sql 2017-04-21 10:55 1.5K
cytoBandIdeo.txt.gz 2017-04-21 10:55 338K
grp.sql 2017-04-21 10:55 1.3K
grp.txt.gz 2017-04-21 10:55 205
development.sql 2017-04-21 10:55 1.4K
development.txt.gz 2017-04-21 10:55 63
history.sql 2017-04-21 10:55 1.6K
history.txt.gz 2017-04-21 10:55 568
netMm10.sql 2017-04-21 10:55 2.1K
netMm10.txt.gz 2017-04-21 10:56 51M
gap.sql 2017-04-21 10:58 1.6K
gap.txt.gz 2017-04-21 10:58 1.5M
imageClone.sql 2017-04-21 10:58 1.5K
imageClone.txt.gz 2017-04-21 10:58 35
organism.sql 2017-04-21 10:58 1.4K
organism.txt.gz 2017-04-21 10:58 307K
gbMiscDiff.sql 2017-04-21 10:58 1.5K
gbMiscDiff.txt.gz 2017-04-21 10:58 1.5K
sex.sql 2017-04-21 11:00 1.4K
sex.txt.gz 2017-04-21 11:00 39
simpleRepeat.sql 2017-04-21 11:00 1.9K
simpleRepeat.txt.gz 2017-04-21 11:00 13M
source.sql 2017-04-21 11:01 1.4K
source.txt.gz 2017-04-21 11:01 312K
tissue.sql 2017-04-21 11:01 1.4K
tissue.txt.gz 2017-04-21 11:01 243
ucscToINSDC.sql 2017-04-21 11:01 1.4K
ucscToINSDC.txt.gz 2017-04-21 11:01 559K
windowmaskerSdust.sql 2017-04-21 11:01 1.5K
windowmaskerSdust.txt.gz 2017-04-21 11:02 103M
gbSeq.sql 2017-12-31 08:30 1.7K
gbSeq.txt.gz 2017-12-31 08:30 13M
gbStatus.sql 2017-12-31 08:30 1.9K
gbStatus.txt.gz 2017-12-31 08:30 4.0M
author.sql 2017-12-31 08:30 1.4K
author.txt.gz 2017-12-31 08:30 4.2M
geneName.sql 2017-12-31 08:30 1.4K
geneName.txt.gz 2017-12-31 08:30 2.8M
cds.sql 2017-12-31 08:30 1.4K
cds.txt.gz 2017-12-31 08:30 2.1M
productName.sql 2017-12-31 08:30 1.4K
description.sql 2017-12-31 08:30 1.4K
productName.txt.gz 2017-12-31 08:30 3.6M
description.txt.gz 2017-12-31 08:30 13M
gbCdnaInfo.sql 2017-12-31 08:30 2.6K
gbCdnaInfo.txt.gz 2017-12-31 08:30 9.2M
refSeqSummary.sql 2017-12-31 08:30 1.5K
refSeqSummary.txt.gz 2017-12-31 08:30 5.3M
refSeqStatus.sql 2017-12-31 08:31 1.6K
refSeqStatus.txt.gz 2017-12-31 08:31 1.5M
gbExtFile.sql 2017-12-31 08:31 1.4K
gbExtFile.txt.gz 2017-12-31 08:31 11K
refLink.sql 2017-12-31 08:31 1.7K
refLink.txt.gz 2017-12-31 08:31 11M
xenoRefGene.sql 2020-08-19 16:12 2.0K
xenoRefGene.txt.gz 2020-08-19 16:12 35M
xenoRefFlat.sql 2020-08-19 16:12 1.7K
xenoRefFlat.txt.gz 2020-08-19 16:12 32M
xenoRefSeqAli.sql 2020-08-19 16:12 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 16:12 37M
gbLoaded.sql 2020-08-19 16:13 1.6K
gbLoaded.txt.gz 2020-08-19 16:13 7.6K
chainMm39.sql 2020-11-24 05:07 1.7K
chainMm39.txt.gz 2020-11-24 05:07 50M
chainMm39Link.sql 2020-11-24 05:10 1.6K
chainMm39Link.txt.gz 2020-11-24 05:10 424M
netMm39.sql 2020-11-24 05:13 2.1K
netMm39.txt.gz 2020-11-24 05:13 52M
trackDb_pushedout.sql 2023-03-28 13:50 2.1K
trackDb_pushedout.txt.gz 2023-03-28 13:50 37K
hgFindSpec_pushedout.sql 2023-03-28 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-03-28 13:50 584
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 37K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 583
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 6.8K
tableList.sql 2024-04-14 03:07 1.6K
tableList.txt.gz 2024-04-14 03:07 3.4K
bigFiles.sql 2024-04-14 03:07 1.4K
bigFiles.txt.gz 2024-04-14 03:07 69