This directory contains a dump of the UCSC genome annotation database for the
Jan. 2018 (Clint_PTRv2/panTro6) assembly of the chimp genome
(panTro6, University of Washington)
from the Chimp Genome Sequencing Consortium.
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/202
https://www.ncbi.nlm.nih.gov/genome/assembly/1642151
https://www.ncbi.nlm.nih.gov/bioproject/369439
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=panTro6
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/panTro6/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/panTro6/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/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 panTro6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro6 --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 -
gc5BaseBw.txt.gz 2018-10-04 12:50 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
bigFiles.txt.gz 2024-11-17 03:14 95
grp.txt.gz 2018-10-04 12:49 213
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
gc5BaseBw.sql 2018-10-04 12:50 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
grp.sql 2018-10-04 12:49 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
chromInfo.sql 2018-10-04 12:49 1.4K
bigFiles.sql 2024-11-17 03:14 1.4K
chromAlias.sql 2018-10-04 12:49 1.4K
ucscToINSDC.sql 2018-10-04 12:50 1.4K
ucscToRefSeq.sql 2018-10-04 12:50 1.4K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.5K
microsat.sql 2018-10-04 12:50 1.5K
windowmaskerSdust.sql 2018-10-04 12:50 1.5K
cytoBandIdeo.sql 2018-10-04 12:49 1.5K
chainHg38Link.sql 2018-10-04 12:45 1.5K
chainMm10Link.sql 2018-10-04 12:46 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
chainMm39Link.sql 2020-11-24 11:17 1.6K
chainNeoSch1Link.sql 2020-07-10 07:01 1.6K
tableList.sql 2024-11-17 03:14 1.6K
gap.sql 2018-10-04 12:49 1.6K
gold.sql 2018-10-04 12:50 1.7K
genscan.sql 2018-10-04 12:50 1.7K
cpgIslandExt.sql 2018-10-04 12:49 1.7K
chainHg38.sql 2018-10-04 12:45 1.7K
chainMm10.sql 2018-10-04 12:46 1.7K
refFlat.sql 2018-10-04 12:46 1.7K
cpgIslandExtUnmasked.sql 2018-10-04 12:49 1.7K
xenoRefFlat.sql 2018-10-04 12:52 1.7K
chainMm39.sql 2020-11-24 11:13 1.7K
chainNeoSch1.sql 2020-07-10 06:54 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
estOrientInfo.sql 2018-10-04 12:49 1.8K
mrnaOrientInfo.sql 2018-10-04 12:50 1.8K
rmsk.sql 2018-10-04 12:49 1.9K
refGene.sql 2018-10-04 12:49 1.9K
simpleRepeat.sql 2018-10-04 12:50 1.9K
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
nestedRepeats.sql 2018-10-04 12:44 1.9K
xenoRefGene.sql 2018-10-04 12:52 1.9K
augustusGene.sql 2018-10-04 12:44 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2018-10-04 12:44 2.1K
netMm10.sql 2018-10-04 12:44 2.1K
all_est.sql 2018-10-04 12:44 2.1K
all_mrna.sql 2018-10-04 12:44 2.1K
xenoMrna.sql 2018-10-04 12:51 2.1K
intronEst.sql 2018-10-04 12:45 2.1K
refSeqAli.sql 2018-10-04 12:49 2.1K
netMm39.sql 2020-11-24 11:20 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
netNeoSch1.sql 2020-07-10 07:05 2.1K
xenoRefSeqAli.sql 2018-10-04 12:52 2.1K
tableList.txt.gz 2024-11-17 03:14 3.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.1K
gap.txt.gz 2018-10-04 12:49 12K
chromInfo.txt.gz 2018-10-04 12:49 25K
cytoBandIdeo.txt.gz 2018-10-04 12:49 25K
ucscToINSDC.txt.gz 2018-10-04 12:50 36K
ucscToRefSeq.txt.gz 2018-10-04 12:50 37K
chromAlias.txt.gz 2018-10-04 12:49 42K
trackDb.txt.gz 2024-01-31 15:13 51K
gold.txt.gz 2018-10-04 12:50 68K
mrnaOrientInfo.txt.gz 2018-10-04 12:50 111K
refFlat.txt.gz 2018-10-04 12:46 201K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 207K
refSeqAli.txt.gz 2018-10-04 12:49 216K
refGene.txt.gz 2018-10-04 12:49 218K
estOrientInfo.txt.gz 2018-10-04 12:49 225K
all_mrna.txt.gz 2018-10-04 12:44 297K
microsat.txt.gz 2018-10-04 12:50 316K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 578K
cpgIslandExt.txt.gz 2018-10-04 12:49 634K
intronEst.txt.gz 2018-10-04 12:45 689K
all_est.txt.gz 2018-10-04 12:44 869K
cpgIslandExtUnmasked.txt.gz 2018-10-04 12:49 1.0M
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.5M
augustusGene.txt.gz 2018-10-04 12:44 2.3M
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.6M
genscan.txt.gz 2018-10-04 12:50 2.9M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.4M
ncbiRefSeq.txt.gz 2020-05-10 03:28 4.5M
netHg38.txt.gz 2018-10-04 12:44 6.4M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 6.8M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 14M
nestedRepeats.txt.gz 2018-10-04 12:44 18M
xenoRefSeqAli.txt.gz 2018-10-04 12:52 19M
xenoRefFlat.txt.gz 2018-10-04 12:52 20M
xenoRefGene.txt.gz 2018-10-04 12:52 22M
simpleRepeat.txt.gz 2018-10-04 12:50 27M
chainMm10.txt.gz 2018-10-04 12:46 63M
chainMm39.txt.gz 2020-11-24 11:13 64M
chainHg38.txt.gz 2018-10-04 12:45 67M
netMm10.txt.gz 2018-10-04 12:45 73M
netMm39.txt.gz 2020-11-24 11:20 73M
netNeoSch1.txt.gz 2020-07-10 07:05 76M
rmsk.txt.gz 2018-10-04 12:49 140M
windowmaskerSdust.txt.gz 2018-10-04 12:50 147M
chainHg38Link.txt.gz 2018-10-04 12:45 214M
chainNeoSch1.txt.gz 2020-07-10 06:54 229M
xenoMrna.txt.gz 2018-10-04 12:51 231M
chainMm39Link.txt.gz 2020-11-24 11:17 512M
chainMm10Link.txt.gz 2018-10-04 12:47 515M
chainNeoSch1Link.txt.gz 2020-07-10 07:01 882M