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 -
all_est.sql 2019-06-25 11:24 2.1K
all_est.txt.gz 2019-06-25 11:24 6.0M
netMm10.sql 2019-06-25 11:24 2.1K
netMm10.txt.gz 2019-06-25 11:24 71M
all_mrna.sql 2019-06-25 11:25 2.1K
all_mrna.txt.gz 2019-06-25 11:25 34K
augustusGene.sql 2019-06-25 11:25 1.9K
augustusGene.txt.gz 2019-06-25 11:25 2.3M
refFlat.sql 2019-06-25 11:25 1.7K
refFlat.txt.gz 2019-06-25 11:25 41K
chainHg38.sql 2019-06-25 11:25 1.7K
chainHg38.txt.gz 2019-06-25 11:25 541M
chainHg38Link.sql 2019-06-25 11:27 1.5K
grp.sql 2019-06-25 11:27 1.3K
grp.txt.gz 2019-06-25 11:27 213
refGene.sql 2019-06-25 11:27 1.9K
refGene.txt.gz 2019-06-25 11:27 45K
chainHg38Link.txt.gz 2019-06-25 11:29 1.5G
chainMm10.sql 2019-06-25 11:34 1.7K
chainMm10.txt.gz 2019-06-25 11:34 65M
chainMm10Link.sql 2019-06-25 11:34 1.5K
refSeqAli.sql 2019-06-25 11:34 2.1K
refSeqAli.txt.gz 2019-06-25 11:34 47K
chainMm10Link.txt.gz 2019-06-25 11:35 501M
chromAlias.sql 2019-06-25 11:37 1.4K
chromAlias.txt.gz 2019-06-25 11:37 651K
chromInfo.sql 2019-06-25 11:37 1.4K
chromInfo.txt.gz 2019-06-25 11:37 328K
history.sql 2019-06-25 11:37 1.6K
history.txt.gz 2019-06-25 11:37 817
rmsk.sql 2019-06-25 11:37 1.9K
rmsk.txt.gz 2019-06-25 11:37 143M
intronEst.sql 2019-06-25 11:37 2.1K
intronEst.txt.gz 2019-06-25 11:37 3.0M
cpgIslandExt.sql 2019-06-25 11:38 1.7K
cpgIslandExt.txt.gz 2019-06-25 11:38 660K
cpgIslandExtUnmasked.sql 2019-06-25 11:38 1.7K
cpgIslandExtUnmasked.txt.gz 2019-06-25 11:38 1.8M
cytoBandIdeo.sql 2019-06-25 11:38 1.5K
cytoBandIdeo.txt.gz 2019-06-25 11:38 320K
gap.sql 2019-06-25 11:38 1.6K
gap.txt.gz 2019-06-25 11:38 703K
microsat.sql 2019-06-25 11:38 1.5K
microsat.txt.gz 2019-06-25 11:38 312K
simpleRepeat.sql 2019-06-25 11:38 1.9K
simpleRepeat.txt.gz 2019-06-25 11:38 30M
mrnaOrientInfo.sql 2019-06-25 11:38 1.8K
mrnaOrientInfo.txt.gz 2019-06-25 11:38 17K
nestedRepeats.sql 2019-06-25 11:38 1.9K
nestedRepeats.txt.gz 2019-06-25 11:38 18M
estOrientInfo.sql 2019-06-25 11:38 1.8K
estOrientInfo.txt.gz 2019-06-25 11:38 1.7M
netHg38.sql 2019-06-25 11:38 2.1K
netHg38.txt.gz 2019-06-25 11:38 28M
gbLoaded.sql 2019-06-25 11:38 1.6K
gbLoaded.txt.gz 2019-06-25 11:38 12K
gc5BaseBw.sql 2019-06-25 11:38 1.3K
gc5BaseBw.txt.gz 2019-06-25 11:38 66
genscan.sql 2019-06-25 11:38 1.7K
genscan.txt.gz 2019-06-25 11:38 2.9M
ucscToINSDC.sql 2019-06-25 11:38 1.4K
ucscToINSDC.txt.gz 2019-06-25 11:38 506K
ucscToRefSeq.sql 2019-06-25 11:38 1.4K
ucscToRefSeq.txt.gz 2019-06-25 11:38 496K
gold.sql 2019-06-25 11:38 1.7K
gold.txt.gz 2019-06-25 11:38 1.6M
windowmaskerSdust.sql 2019-06-25 11:38 1.5K
windowmaskerSdust.txt.gz 2019-06-25 11:38 147M
xenoRefFlat.sql 2019-06-25 11:39 1.7K
xenoRefFlat.txt.gz 2019-06-25 11:39 22M
xenoRefGene.sql 2019-06-25 11:39 1.9K
xenoRefGene.txt.gz 2019-06-25 11:39 25M
xenoRefSeqAli.sql 2019-06-25 11:39 2.1K
xenoRefSeqAli.txt.gz 2019-06-25 11:39 23M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 4.0M
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 473K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 44K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.2M
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 12M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.0M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.7M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.3M
ensGene.sql 2021-05-25 14:43 1.9K
ensGene.txt.gz 2021-05-25 14:43 3.1M
ensGtp.sql 2021-05-25 14:43 1.4K
ensGtp.txt.gz 2021-05-25 14:43 522K
ensemblToGeneName.sql 2021-05-25 14:43 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:43 264K
ensemblSource.sql 2021-05-25 14:43 1.4K
ensemblSource.txt.gz 2021-05-25 14:43 158K
ensPep.sql 2021-05-25 14:43 1.3K
ensPep.txt.gz 2021-05-25 14:43 14M
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 32K
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.3K
tableDescriptions.sql 2024-11-23 02:04 1.5K
tableDescriptions.txt.gz 2024-11-23 02:04 6.3K
tableList.sql 2024-11-24 03:04 1.6K
tableList.txt.gz 2024-11-24 03:04 3.2K
bigFiles.sql 2024-11-24 03:04 1.4K
bigFiles.txt.gz 2024-11-24 03:04 95