This directory contains a dump of the UCSC genome annotation database for the
Apr. 2017 (Panu_3.0/papAnu4) assembly of the baboon genome
(papAnu4, Human Genome Sequencing Center) .
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/394
https://www.ncbi.nlm.nih.gov/genome/assembly/1082401
https://www.ncbi.nlm.nih.gov/bioproject/54005
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=papAnu4
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/papAnu4/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/papAnu4/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/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 papAnu4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papAnu4 --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 -
chainHg38Link.txt.gz 2019-06-25 11:29 1.5G
chainHg38.txt.gz 2019-06-25 11:25 541M
chainMm10Link.txt.gz 2019-06-25 11:35 501M
windowmaskerSdust.txt.gz 2019-06-25 11:38 147M
rmsk.txt.gz 2019-06-25 11:37 143M
netMm10.txt.gz 2019-06-25 11:24 71M
chainMm10.txt.gz 2019-06-25 11:34 65M
simpleRepeat.txt.gz 2019-06-25 11:38 30M
netHg38.txt.gz 2019-06-25 11:38 28M
xenoRefGene.txt.gz 2019-06-25 11:39 25M
xenoRefSeqAli.txt.gz 2019-06-25 11:39 23M
xenoRefFlat.txt.gz 2019-06-25 11:39 22M
nestedRepeats.txt.gz 2019-06-25 11:38 18M
ensPep.txt.gz 2021-05-25 14:43 14M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 12M
all_est.txt.gz 2019-06-25 11:24 6.0M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.7M
ncbiRefSeq.txt.gz 2020-05-10 03:28 4.0M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.0M
ensGene.txt.gz 2021-05-25 14:43 3.1M
intronEst.txt.gz 2019-06-25 11:37 3.0M
genscan.txt.gz 2019-06-25 11:38 2.9M
augustusGene.txt.gz 2019-06-25 11:25 2.3M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.2M
cpgIslandExtUnmasked.txt.gz 2019-06-25 11:38 1.8M
estOrientInfo.txt.gz 2019-06-25 11:38 1.7M
gold.txt.gz 2019-06-25 11:38 1.6M
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.3M
gap.txt.gz 2019-06-25 11:38 703K
cpgIslandExt.txt.gz 2019-06-25 11:38 660K
chromAlias.txt.gz 2019-06-25 11:37 651K
ensGtp.txt.gz 2021-05-25 14:43 522K
ucscToINSDC.txt.gz 2019-06-25 11:38 506K
ucscToRefSeq.txt.gz 2019-06-25 11:38 496K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 473K
chromInfo.txt.gz 2019-06-25 11:37 328K
cytoBandIdeo.txt.gz 2019-06-25 11:38 320K
microsat.txt.gz 2019-06-25 11:38 312K
ensemblToGeneName.txt.gz 2021-05-25 14:43 264K
ensemblSource.txt.gz 2021-05-25 14:43 158K
refSeqAli.txt.gz 2019-06-25 11:34 47K
refGene.txt.gz 2019-06-25 11:27 45K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 44K
refFlat.txt.gz 2019-06-25 11:25 41K
all_mrna.txt.gz 2019-06-25 11:25 34K
trackDb.txt.gz 2023-12-05 13:51 32K
mrnaOrientInfo.txt.gz 2019-06-25 11:38 17K
gbLoaded.txt.gz 2019-06-25 11:38 12K
tableDescriptions.txt.gz 2024-11-02 02:04 6.3K
tableList.txt.gz 2024-11-03 03:05 3.2K
xenoRefSeqAli.sql 2019-06-25 11:39 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
refSeqAli.sql 2019-06-25 11:34 2.1K
intronEst.sql 2019-06-25 11:37 2.1K
all_mrna.sql 2019-06-25 11:25 2.1K
all_est.sql 2019-06-25 11:24 2.1K
netMm10.sql 2019-06-25 11:24 2.1K
netHg38.sql 2019-06-25 11:38 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
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ensGene.sql 2021-05-25 14:43 1.9K
augustusGene.sql 2019-06-25 11:25 1.9K
xenoRefGene.sql 2019-06-25 11:39 1.9K
nestedRepeats.sql 2019-06-25 11:38 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
simpleRepeat.sql 2019-06-25 11:38 1.9K
refGene.sql 2019-06-25 11:27 1.9K
rmsk.sql 2019-06-25 11:37 1.9K
mrnaOrientInfo.sql 2019-06-25 11:38 1.8K
estOrientInfo.sql 2019-06-25 11:38 1.8K
hgFindSpec.sql 2023-12-05 13:51 1.8K
xenoRefFlat.sql 2019-06-25 11:39 1.7K
cpgIslandExtUnmasked.sql 2019-06-25 11:38 1.7K
refFlat.sql 2019-06-25 11:25 1.7K
chainMm10.sql 2019-06-25 11:34 1.7K
chainHg38.sql 2019-06-25 11:25 1.7K
cpgIslandExt.sql 2019-06-25 11:38 1.7K
genscan.sql 2019-06-25 11:38 1.7K
gold.sql 2019-06-25 11:38 1.7K
gap.sql 2019-06-25 11:38 1.6K
gbLoaded.sql 2019-06-25 11:38 1.6K
history.sql 2019-06-25 11:37 1.6K
tableList.sql 2024-11-03 03:05 1.6K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
chainMm10Link.sql 2019-06-25 11:34 1.5K
chainHg38Link.sql 2019-06-25 11:27 1.5K
cytoBandIdeo.sql 2019-06-25 11:38 1.5K
windowmaskerSdust.sql 2019-06-25 11:38 1.5K
microsat.sql 2019-06-25 11:38 1.5K
ensGtp.sql 2021-05-25 14:43 1.4K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ucscToRefSeq.sql 2019-06-25 11:38 1.4K
tableDescriptions.sql 2024-11-02 02:04 1.4K
ucscToINSDC.sql 2019-06-25 11:38 1.4K
chromAlias.sql 2019-06-25 11:37 1.4K
ensemblToGeneName.sql 2021-05-25 14:43 1.4K
chromInfo.sql 2019-06-25 11:37 1.4K
bigFiles.sql 2024-11-03 03:05 1.4K
ensemblSource.sql 2021-05-25 14:43 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
grp.sql 2019-06-25 11:27 1.3K
ensPep.sql 2021-05-25 14:43 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
gc5BaseBw.sql 2019-06-25 11:38 1.3K
hgFindSpec.txt.gz 2023-12-05 13:51 1.3K
history.txt.gz 2019-06-25 11:37 817
grp.txt.gz 2019-06-25 11:27 213
bigFiles.txt.gz 2024-11-03 03:05 95
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
gc5BaseBw.txt.gz 2019-06-25 11:38 66