This directory contains a dump of the UCSC genome annotation database for the
Feb. 2019 (Mmul_10/rheMac10) assembly of the rhesus genome
(rheMac10, The Genome Institute at Washington University School of Medicine) .
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/215
https://www.ncbi.nlm.nih.gov/genome/assembly/2345051
https://www.ncbi.nlm.nih.gov/bioproject/476474
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=rheMac10
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/rheMac10/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/rheMac10/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/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 rheMac10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rheMac10 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Rhesus 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.
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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 2019-09-03 15:33 67
rhesusSNVs.txt.gz 2020-05-19 14:27 72
ncbiRefSeqOther.txt.gz 2019-09-03 15:27 76
extNcbiRefSeq.txt.gz 2019-09-03 15:33 89
gapOverlap.txt.gz 2019-09-03 15:33 91
bigFiles.txt.gz 2024-11-17 03:13 124
grp.txt.gz 2019-09-03 15:33 213
history.txt.gz 2019-09-03 15:29 941
gbLoaded.txt.gz 2019-09-03 15:33 944
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
gc5BaseBw.sql 2019-09-03 15:33 1.3K
ncbiRefSeqOther.sql 2019-09-03 15:27 1.3K
rhesusSNVs.sql 2020-05-19 14:27 1.3K
ncbiRefSeqCds.sql 2019-09-03 15:33 1.3K
ensPep.sql 2021-05-25 14:49 1.3K
grp.sql 2019-09-03 15:33 1.3K
ncbiRefSeqPepTable.sql 2019-09-03 15:34 1.4K
ensemblSource.sql 2021-05-25 14:49 1.4K
chromInfo.sql 2019-09-03 15:33 1.4K
bigFiles.sql 2024-11-17 03:13 1.4K
ensemblToGeneName.sql 2021-05-25 14:47 1.4K
chromAlias.sql 2019-09-03 15:33 1.4K
ucscToINSDC.sql 2019-09-03 15:34 1.4K
ucscToRefSeq.sql 2019-09-03 15:34 1.4K
extNcbiRefSeq.sql 2019-09-03 15:33 1.4K
ensGtp.sql 2021-05-25 14:47 1.4K
tableDescriptions.sql 2024-11-16 02:04 1.5K
microsat.sql 2019-09-03 15:33 1.5K
windowmaskerSdust.sql 2019-09-03 15:34 1.5K
cytoBandIdeo.sql 2019-09-03 15:33 1.5K
chainHg19Link.sql 2019-09-03 15:27 1.5K
chainHg38Link.sql 2019-09-03 15:29 1.5K
chainMm10Link.sql 2019-09-03 15:30 1.5K
seqNcbiRefSeq.sql 2019-09-03 15:34 1.5K
chainMm39Link.sql 2020-10-21 09:12 1.6K
chainNeoSch1Link.sql 2020-07-12 01:26 1.6K
history.sql 2019-09-03 15:29 1.6K
gbLoaded.sql 2019-09-03 15:33 1.6K
tableList.sql 2024-11-17 03:13 1.6K
gap.sql 2019-09-03 15:33 1.6K
gold.sql 2019-09-03 15:33 1.7K
genscan.sql 2019-09-03 15:33 1.7K
cpgIslandExt.sql 2019-09-03 15:33 1.7K
chainHg19.sql 2019-09-03 15:27 1.7K
chainHg38.sql 2019-09-03 15:29 1.7K
chainMm10.sql 2019-09-03 15:30 1.7K
refFlat.sql 2019-09-03 15:33 1.7K
cpgIslandExtUnmasked.sql 2019-09-03 15:33 1.7K
xenoRefFlat.sql 2019-09-03 15:35 1.7K
chainMm39.sql 2020-10-21 09:09 1.7K
chainNeoSch1.sql 2020-07-12 01:20 1.7K
estOrientInfo.sql 2019-09-03 15:33 1.8K
mrnaOrientInfo.sql 2019-09-03 15:33 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
gapOverlap.sql 2019-09-03 15:33 1.8K
tandemDups.sql 2019-09-03 15:34 1.8K
rmsk.sql 2019-09-03 15:33 1.9K
refGene.sql 2019-09-03 15:33 1.9K
simpleRepeat.sql 2019-09-03 15:34 1.9K
ncbiRefSeq.sql 2019-09-03 15:33 1.9K
nestedRepeats.sql 2019-09-03 15:28 1.9K
xenoRefGene.sql 2019-09-03 15:35 1.9K
augustusGene.sql 2019-09-03 15:27 1.9K
ensGene.sql 2021-05-25 14:47 1.9K
ncbiRefSeqCurated.sql 2019-09-03 15:33 2.0K
ncbiRefSeqPredicted.sql 2019-09-03 15:34 2.0K
ncbiRefSeqLink.sql 2019-09-03 15:27 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netHg19.sql 2019-09-03 15:29 2.1K
netHg38.sql 2019-09-03 15:33 2.1K
netMm10.sql 2019-09-03 15:33 2.1K
all_est.sql 2019-09-03 15:27 2.1K
all_mrna.sql 2019-09-03 15:27 2.1K
intronEst.sql 2019-09-03 15:30 2.1K
refSeqAli.sql 2019-09-03 15:33 2.1K
netMm39.sql 2020-10-21 09:16 2.1K
ncbiRefSeqPsl.sql 2019-09-03 15:27 2.1K
xenoRefSeqAli.sql 2019-09-03 15:35 2.1K
netNeoSch1.sql 2020-07-12 01:29 2.1K
tableList.txt.gz 2024-11-17 03:13 3.8K
gap.txt.gz 2019-09-03 15:33 4.1K
tableDescriptions.txt.gz 2024-11-16 02:04 6.7K
cytoBandIdeo.txt.gz 2019-09-03 15:33 18K
chromInfo.txt.gz 2019-09-03 15:33 19K
ucscToRefSeq.txt.gz 2019-09-03 15:34 25K
ucscToINSDC.txt.gz 2019-09-03 15:34 25K
chromAlias.txt.gz 2019-09-03 15:33 28K
gold.txt.gz 2019-09-03 15:33 41K
trackDb.txt.gz 2024-07-25 09:34 72K
ensemblSource.txt.gz 2021-05-25 14:49 197K
ensemblToGeneName.txt.gz 2021-05-25 14:47 322K
microsat.txt.gz 2019-09-03 15:33 352K
ncbiRefSeqCds.txt.gz 2019-09-03 15:33 469K
refFlat.txt.gz 2019-09-03 15:33 503K
ncbiRefSeqCurated.txt.gz 2019-09-03 15:33 550K
refGene.txt.gz 2019-09-03 15:33 552K
refSeqAli.txt.gz 2019-09-03 15:33 563K
cpgIslandExt.txt.gz 2019-09-03 15:33 634K
ensGtp.txt.gz 2021-05-25 14:47 673K
estOrientInfo.txt.gz 2019-09-03 15:33 937K
seqNcbiRefSeq.txt.gz 2019-09-03 15:34 1.3M
cpgIslandExtUnmasked.txt.gz 2019-09-03 15:33 1.6M
intronEst.txt.gz 2019-09-03 15:30 2.2M
ncbiRefSeqLink.txt.gz 2019-09-03 15:27 2.3M
augustusGene.txt.gz 2019-09-03 15:27 2.3M
genscan.txt.gz 2019-09-03 15:33 2.9M
ensGene.txt.gz 2021-05-25 14:47 3.6M
ncbiRefSeqPredicted.txt.gz 2019-09-03 15:34 3.8M
all_est.txt.gz 2019-09-03 15:27 4.0M
ncbiRefSeq.txt.gz 2019-09-03 15:33 4.1M
mrnaOrientInfo.txt.gz 2019-09-03 15:33 4.2M
ncbiRefSeqPsl.txt.gz 2019-09-03 15:27 5.9M
ncbiRefSeqPepTable.txt.gz 2019-09-03 15:34 12M
xenoRefFlat.txt.gz 2019-09-03 15:35 14M
all_mrna.txt.gz 2019-09-03 15:27 16M
xenoRefGene.txt.gz 2019-09-03 15:35 16M
ensPep.txt.gz 2021-05-25 14:49 16M
nestedRepeats.txt.gz 2019-09-03 15:28 18M
chainHg19.txt.gz 2019-09-03 15:27 19M
chainHg38.txt.gz 2019-09-03 15:29 21M
netHg19.txt.gz 2019-09-03 15:29 22M
netHg38.txt.gz 2019-09-03 15:33 22M
xenoRefSeqAli.txt.gz 2019-09-03 15:35 22M
simpleRepeat.txt.gz 2019-09-03 15:34 26M
tandemDups.txt.gz 2019-09-03 15:34 30M
chainMm39.txt.gz 2020-10-21 09:09 64M
chainMm10.txt.gz 2019-09-03 15:30 67M
netMm10.txt.gz 2019-09-03 15:33 72M
netMm39.txt.gz 2020-10-21 09:16 72M
netNeoSch1.txt.gz 2020-07-12 01:29 77M
rmsk.txt.gz 2019-09-03 15:33 141M
windowmaskerSdust.txt.gz 2019-09-03 15:34 146M
chainHg19Link.txt.gz 2019-09-03 15:28 205M
chainNeoSch1.txt.gz 2020-07-12 01:20 206M
chainHg38Link.txt.gz 2019-09-03 15:29 210M
chainMm39Link.txt.gz 2020-10-21 09:12 500M
chainMm10Link.txt.gz 2019-09-03 15:31 514M
chainNeoSch1Link.txt.gz 2020-07-12 01:26 846M