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 -
gbWarn.txt.gz 2017-04-21 09:35 31
imageClone.txt.gz 2017-04-21 10:58 35
sex.txt.gz 2017-04-21 11:00 39
cell.txt.gz 2017-04-21 09:35 40
library.txt.gz 2017-04-21 09:35 43
development.txt.gz 2017-04-21 10:55 63
gc5BaseBw.txt.gz 2017-04-21 10:23 66
bigFiles.txt.gz 2024-11-17 03:15 69
grp.txt.gz 2017-04-21 10:55 205
tissue.txt.gz 2017-04-21 11:01 243
history.txt.gz 2017-04-21 10:55 568
hgFindSpec.txt.gz 2024-01-31 15:13 583
keyword.txt.gz 2017-04-21 09:35 778
gc5BaseBw.sql 2017-04-21 10:23 1.3K
gbWarn.sql 2017-04-21 09:35 1.3K
grp.sql 2017-04-21 10:55 1.3K
bigFiles.sql 2024-11-17 03:15 1.4K
chromInfo.sql 2017-04-21 10:51 1.4K
cds.sql 2017-12-31 08:30 1.4K
sex.sql 2017-04-21 11:00 1.4K
cell.sql 2017-04-21 09:35 1.4K
author.sql 2017-12-31 08:30 1.4K
source.sql 2017-04-21 11:01 1.4K
tissue.sql 2017-04-21 11:01 1.4K
gbExtFile.sql 2017-12-31 08:31 1.4K
keyword.sql 2017-04-21 09:35 1.4K
library.sql 2017-04-21 09:35 1.4K
geneName.sql 2017-12-31 08:30 1.4K
organism.sql 2017-04-21 10:58 1.4K
mrnaClone.sql 2017-04-21 09:35 1.4K
description.sql 2017-12-31 08:30 1.4K
development.sql 2017-04-21 10:55 1.4K
productName.sql 2017-12-31 08:30 1.4K
chromAlias.sql 2017-04-21 10:48 1.4K
ucscToINSDC.sql 2017-04-21 11:01 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
mrnaClone.txt.gz 2017-04-21 09:35 1.4K
gbMiscDiff.sql 2017-04-21 10:58 1.5K
gbMiscDiff.txt.gz 2017-04-21 10:58 1.5K
microsat.sql 2017-04-21 09:35 1.5K
refSeqSummary.sql 2017-12-31 08:30 1.5K
imageClone.sql 2017-04-21 10:58 1.5K
windowmaskerSdust.sql 2017-04-21 11:01 1.5K
cytoBandIdeo.sql 2017-04-21 10:55 1.5K
chainHg38Link.sql 2017-04-21 09:46 1.5K
chainMm10Link.sql 2017-04-21 10:26 1.5K
chainMm39Link.sql 2020-11-24 05:10 1.6K
tableList.sql 2024-11-17 03:15 1.6K
history.sql 2017-04-21 10:55 1.6K
gap.sql 2017-04-21 10:58 1.6K
refSeqStatus.sql 2017-12-31 08:31 1.6K
gbLoaded.sql 2020-08-19 16:13 1.6K
gold.sql 2017-04-21 10:51 1.7K
genscan.sql 2017-04-21 10:48 1.7K
cpgIslandExt.sql 2017-04-21 10:51 1.7K
chainHg38.sql 2017-04-21 09:35 1.7K
chainMm10.sql 2017-04-21 10:23 1.7K
gbSeq.sql 2017-12-31 08:30 1.7K
cpgIslandExtUnmasked.sql 2017-04-21 10:54 1.7K
chainMm39.sql 2020-11-24 05:07 1.7K
refLink.sql 2017-12-31 08:31 1.7K
xenoRefFlat.sql 2020-08-19 16:12 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
rmsk.sql 2017-04-21 10:51 1.9K
gbStatus.sql 2017-12-31 08:30 1.9K
simpleRepeat.sql 2017-04-21 11:00 1.9K
nestedRepeats.sql 2017-04-21 10:23 1.9K
augustusGene.sql 2017-04-21 09:35 1.9K
xenoRefGene.sql 2020-08-19 16:12 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2017-04-21 10:48 2.1K
netMm10.sql 2017-04-21 10:55 2.1K
netMm39.sql 2020-11-24 05:13 2.1K
xenoRefSeqAli.sql 2020-08-19 16:12 2.1K
gbCdnaInfo.sql 2017-12-31 08:30 2.6K
tableList.txt.gz 2024-11-17 03:15 3.2K
tableDescriptions.txt.gz 2024-11-16 02:03 6.8K
gbLoaded.txt.gz 2020-08-19 16:13 7.6K
gbExtFile.txt.gz 2017-12-31 08:31 11K
trackDb.txt.gz 2024-01-31 15:13 37K
microsat.txt.gz 2017-04-21 09:35 221K
organism.txt.gz 2017-04-21 10:58 307K
source.txt.gz 2017-04-21 11:01 312K
cytoBandIdeo.txt.gz 2017-04-21 10:55 338K
chromInfo.txt.gz 2017-04-21 10:51 365K
chromAlias.txt.gz 2017-04-21 10:48 449K
ucscToINSDC.txt.gz 2017-04-21 11:01 559K
cpgIslandExt.txt.gz 2017-04-21 10:51 564K
cpgIslandExtUnmasked.txt.gz 2017-04-21 10:54 612K
refSeqStatus.txt.gz 2017-12-31 08:31 1.5M
gap.txt.gz 2017-04-21 10:58 1.5M
augustusGene.txt.gz 2017-04-21 09:35 1.9M
cds.txt.gz 2017-12-31 08:30 2.1M
gold.txt.gz 2017-04-21 10:51 2.7M
geneName.txt.gz 2017-12-31 08:30 2.8M
genscan.txt.gz 2017-04-21 10:48 2.8M
productName.txt.gz 2017-12-31 08:30 3.6M
gbStatus.txt.gz 2017-12-31 08:30 4.0M
author.txt.gz 2017-12-31 08:30 4.2M
refSeqSummary.txt.gz 2017-12-31 08:30 5.3M
nestedRepeats.txt.gz 2017-04-21 10:23 7.6M
gbCdnaInfo.txt.gz 2017-12-31 08:30 9.2M
refLink.txt.gz 2017-12-31 08:31 11M
simpleRepeat.txt.gz 2017-04-21 11:00 13M
gbSeq.txt.gz 2017-12-31 08:30 13M
description.txt.gz 2017-12-31 08:30 13M
xenoRefFlat.txt.gz 2020-08-19 16:12 32M
xenoRefGene.txt.gz 2020-08-19 16:12 35M
xenoRefSeqAli.txt.gz 2020-08-19 16:12 37M
netHg38.txt.gz 2017-04-21 10:49 44M
chainMm39.txt.gz 2020-11-24 05:07 50M
netMm10.txt.gz 2017-04-21 10:56 51M
netMm39.txt.gz 2020-11-24 05:13 52M
chainMm10.txt.gz 2017-04-21 10:24 54M
rmsk.txt.gz 2017-04-21 10:52 67M
windowmaskerSdust.txt.gz 2017-04-21 11:02 103M
chainHg38.txt.gz 2017-04-21 09:38 203M
chainMm39Link.txt.gz 2020-11-24 05:10 424M
chainMm10Link.txt.gz 2017-04-21 10:31 441M
chainHg38Link.txt.gz 2017-04-21 09:55 834M