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.
---------------------------------------------------------------
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;'
-----------------------------------------------------------------------------
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 -
bigFiles.txt.gz 2024-11-17 03:14 95
bigFiles.sql 2024-11-17 03:14 1.4K
tableList.txt.gz 2024-11-17 03:14 3.4K
tableList.sql 2024-11-17 03:14 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.1K
tableDescriptions.sql 2024-11-16 02:03 1.5K
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
hgFindSpec.sql 2024-01-31 15:13 1.8K
trackDb.txt.gz 2024-01-31 15:13 51K
trackDb.sql 2024-01-31 15:13 2.1K
netMm39.txt.gz 2020-11-24 11:20 73M
netMm39.sql 2020-11-24 11:20 2.1K
chainMm39Link.txt.gz 2020-11-24 11:17 512M
chainMm39Link.sql 2020-11-24 11:17 1.6K
chainMm39.txt.gz 2020-11-24 11:13 64M
chainMm39.sql 2020-11-24 11:13 1.7K
netNeoSch1.txt.gz 2020-07-10 07:05 76M
netNeoSch1.sql 2020-07-10 07:05 2.1K
chainNeoSch1Link.txt.gz 2020-07-10 07:01 882M
chainNeoSch1Link.sql 2020-07-10 07:01 1.6K
chainNeoSch1.txt.gz 2020-07-10 06:54 229M
chainNeoSch1.sql 2020-07-10 06:54 1.7K
ncbiRefSeq.txt.gz 2020-05-10 03:28 4.5M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.5M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 6.8M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.4M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 14M
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.6M
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 207K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 578K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
xenoRefSeqAli.txt.gz 2018-10-04 12:52 19M
xenoRefSeqAli.sql 2018-10-04 12:52 2.1K
xenoRefGene.txt.gz 2018-10-04 12:52 22M
xenoRefGene.sql 2018-10-04 12:52 1.9K
xenoRefFlat.txt.gz 2018-10-04 12:52 20M
xenoRefFlat.sql 2018-10-04 12:52 1.7K
xenoMrna.txt.gz 2018-10-04 12:51 231M
xenoMrna.sql 2018-10-04 12:51 2.1K
windowmaskerSdust.txt.gz 2018-10-04 12:50 147M
windowmaskerSdust.sql 2018-10-04 12:50 1.5K
ucscToRefSeq.txt.gz 2018-10-04 12:50 37K
ucscToRefSeq.sql 2018-10-04 12:50 1.4K
ucscToINSDC.txt.gz 2018-10-04 12:50 36K
ucscToINSDC.sql 2018-10-04 12:50 1.4K
mrnaOrientInfo.txt.gz 2018-10-04 12:50 111K
mrnaOrientInfo.sql 2018-10-04 12:50 1.8K
microsat.txt.gz 2018-10-04 12:50 316K
microsat.sql 2018-10-04 12:50 1.5K
gold.txt.gz 2018-10-04 12:50 68K
gold.sql 2018-10-04 12:50 1.7K
simpleRepeat.txt.gz 2018-10-04 12:50 27M
simpleRepeat.sql 2018-10-04 12:50 1.9K
genscan.txt.gz 2018-10-04 12:50 2.9M
genscan.sql 2018-10-04 12:50 1.7K
gc5BaseBw.txt.gz 2018-10-04 12:50 66
gc5BaseBw.sql 2018-10-04 12:50 1.3K
rmsk.txt.gz 2018-10-04 12:49 140M
rmsk.sql 2018-10-04 12:49 1.9K
refSeqAli.txt.gz 2018-10-04 12:49 216K
refSeqAli.sql 2018-10-04 12:49 2.1K
gap.txt.gz 2018-10-04 12:49 12K
gap.sql 2018-10-04 12:49 1.6K
estOrientInfo.txt.gz 2018-10-04 12:49 225K
estOrientInfo.sql 2018-10-04 12:49 1.8K
grp.txt.gz 2018-10-04 12:49 213
grp.sql 2018-10-04 12:49 1.3K
cytoBandIdeo.txt.gz 2018-10-04 12:49 25K
cytoBandIdeo.sql 2018-10-04 12:49 1.5K
cpgIslandExtUnmasked.txt.gz 2018-10-04 12:49 1.0M
cpgIslandExtUnmasked.sql 2018-10-04 12:49 1.7K
refGene.txt.gz 2018-10-04 12:49 218K
refGene.sql 2018-10-04 12:49 1.9K
cpgIslandExt.txt.gz 2018-10-04 12:49 634K
cpgIslandExt.sql 2018-10-04 12:49 1.7K
chromInfo.txt.gz 2018-10-04 12:49 25K
chromInfo.sql 2018-10-04 12:49 1.4K
chromAlias.txt.gz 2018-10-04 12:49 42K
chromAlias.sql 2018-10-04 12:49 1.4K
chainMm10Link.txt.gz 2018-10-04 12:47 515M
chainMm10Link.sql 2018-10-04 12:46 1.5K
chainMm10.txt.gz 2018-10-04 12:46 63M
refFlat.txt.gz 2018-10-04 12:46 201K
refFlat.sql 2018-10-04 12:46 1.7K
chainMm10.sql 2018-10-04 12:46 1.7K
chainHg38Link.txt.gz 2018-10-04 12:45 214M
intronEst.txt.gz 2018-10-04 12:45 689K
intronEst.sql 2018-10-04 12:45 2.1K
chainHg38Link.sql 2018-10-04 12:45 1.5K
chainHg38.txt.gz 2018-10-04 12:45 67M
chainHg38.sql 2018-10-04 12:45 1.7K
netMm10.txt.gz 2018-10-04 12:45 73M
netMm10.sql 2018-10-04 12:44 2.1K
augustusGene.txt.gz 2018-10-04 12:44 2.3M
augustusGene.sql 2018-10-04 12:44 1.9K
all_mrna.txt.gz 2018-10-04 12:44 297K
all_mrna.sql 2018-10-04 12:44 2.1K
netHg38.txt.gz 2018-10-04 12:44 6.4M
netHg38.sql 2018-10-04 12:44 2.1K
all_est.txt.gz 2018-10-04 12:44 869K
all_est.sql 2018-10-04 12:44 2.1K
nestedRepeats.txt.gz 2018-10-04 12:44 18M
nestedRepeats.sql 2018-10-04 12:44 1.9K