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.
---------------------------------------------------------------
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.
-----------------------------------------------------------------------------
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 -
all_est.sql 2019-09-03 15:27 2.1K
all_est.txt.gz 2019-09-03 15:27 4.0M
all_mrna.sql 2019-09-03 15:27 2.1K
all_mrna.txt.gz 2019-09-03 15:27 16M
augustusGene.sql 2019-09-03 15:27 1.9K
augustusGene.txt.gz 2019-09-03 15:27 2.3M
bigFiles.sql 2024-11-24 03:04 1.4K
bigFiles.txt.gz 2024-11-24 03:04 124
chainHg19.sql 2019-09-03 15:27 1.7K
chainHg19.txt.gz 2019-09-03 15:27 19M
chainHg19Link.sql 2019-09-03 15:27 1.5K
chainHg19Link.txt.gz 2019-09-03 15:28 205M
chainHg38.sql 2019-09-03 15:29 1.7K
chainHg38.txt.gz 2019-09-03 15:29 21M
chainHg38Link.sql 2019-09-03 15:29 1.5K
chainHg38Link.txt.gz 2019-09-03 15:29 210M
chainMm10.sql 2019-09-03 15:30 1.7K
chainMm10.txt.gz 2019-09-03 15:30 67M
chainMm10Link.sql 2019-09-03 15:30 1.5K
chainMm10Link.txt.gz 2019-09-03 15:31 514M
chainMm39.sql 2020-10-21 09:09 1.7K
chainMm39.txt.gz 2020-10-21 09:09 64M
chainMm39Link.sql 2020-10-21 09:12 1.6K
chainMm39Link.txt.gz 2020-10-21 09:12 500M
chainNeoSch1.sql 2020-07-12 01:20 1.7K
chainNeoSch1.txt.gz 2020-07-12 01:20 206M
chainNeoSch1Link.sql 2020-07-12 01:26 1.6K
chainNeoSch1Link.txt.gz 2020-07-12 01:26 846M
chromAlias.sql 2019-09-03 15:33 1.4K
chromAlias.txt.gz 2019-09-03 15:33 28K
chromInfo.sql 2019-09-03 15:33 1.4K
chromInfo.txt.gz 2019-09-03 15:33 19K
cpgIslandExt.sql 2019-09-03 15:33 1.7K
cpgIslandExt.txt.gz 2019-09-03 15:33 634K
cpgIslandExtUnmasked.sql 2019-09-03 15:33 1.7K
cpgIslandExtUnmasked.txt.gz 2019-09-03 15:33 1.6M
cytoBandIdeo.sql 2019-09-03 15:33 1.5K
cytoBandIdeo.txt.gz 2019-09-03 15:33 18K
ensGene.sql 2021-05-25 14:47 1.9K
ensGene.txt.gz 2021-05-25 14:47 3.6M
ensGtp.sql 2021-05-25 14:47 1.4K
ensGtp.txt.gz 2021-05-25 14:47 673K
ensPep.sql 2021-05-25 14:49 1.3K
ensPep.txt.gz 2021-05-25 14:49 16M
ensemblSource.sql 2021-05-25 14:49 1.4K
ensemblSource.txt.gz 2021-05-25 14:49 197K
ensemblToGeneName.sql 2021-05-25 14:47 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:47 322K
estOrientInfo.sql 2019-09-03 15:33 1.8K
estOrientInfo.txt.gz 2019-09-03 15:33 937K
extNcbiRefSeq.sql 2019-09-03 15:33 1.4K
extNcbiRefSeq.txt.gz 2019-09-03 15:33 89
gap.sql 2019-09-03 15:33 1.6K
gap.txt.gz 2019-09-03 15:33 4.1K
gapOverlap.sql 2019-09-03 15:33 1.8K
gapOverlap.txt.gz 2019-09-03 15:33 91
gbLoaded.sql 2019-09-03 15:33 1.6K
gbLoaded.txt.gz 2019-09-03 15:33 944
gc5BaseBw.sql 2019-09-03 15:33 1.3K
gc5BaseBw.txt.gz 2019-09-03 15:33 67
genscan.sql 2019-09-03 15:33 1.7K
genscan.txt.gz 2019-09-03 15:33 2.9M
gold.sql 2019-09-03 15:33 1.7K
gold.txt.gz 2019-09-03 15:33 41K
grp.sql 2019-09-03 15:33 1.3K
grp.txt.gz 2019-09-03 15:33 213
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
history.sql 2019-09-03 15:29 1.6K
history.txt.gz 2019-09-03 15:29 941
intronEst.sql 2019-09-03 15:30 2.1K
intronEst.txt.gz 2019-09-03 15:30 2.2M
microsat.sql 2019-09-03 15:33 1.5K
microsat.txt.gz 2019-09-03 15:33 352K
mrnaOrientInfo.sql 2019-09-03 15:33 1.8K
mrnaOrientInfo.txt.gz 2019-09-03 15:33 4.2M
ncbiRefSeq.sql 2019-09-03 15:33 1.9K
ncbiRefSeq.txt.gz 2019-09-03 15:33 4.1M
ncbiRefSeqCds.sql 2019-09-03 15:33 1.3K
ncbiRefSeqCds.txt.gz 2019-09-03 15:33 469K
ncbiRefSeqCurated.sql 2019-09-03 15:33 2.0K
ncbiRefSeqCurated.txt.gz 2019-09-03 15:33 550K
ncbiRefSeqLink.sql 2019-09-03 15:27 2.0K
ncbiRefSeqLink.txt.gz 2019-09-03 15:27 2.3M
ncbiRefSeqOther.sql 2019-09-03 15:27 1.3K
ncbiRefSeqOther.txt.gz 2019-09-03 15:27 76
ncbiRefSeqPepTable.sql 2019-09-03 15:34 1.4K
ncbiRefSeqPepTable.txt.gz 2019-09-03 15:34 12M
ncbiRefSeqPredicted.sql 2019-09-03 15:34 2.0K
ncbiRefSeqPredicted.txt.gz 2019-09-03 15:34 3.8M
ncbiRefSeqPsl.sql 2019-09-03 15:27 2.1K
ncbiRefSeqPsl.txt.gz 2019-09-03 15:27 5.9M
nestedRepeats.sql 2019-09-03 15:28 1.9K
nestedRepeats.txt.gz 2019-09-03 15:28 18M
netHg19.sql 2019-09-03 15:29 2.1K
netHg19.txt.gz 2019-09-03 15:29 22M
netHg38.sql 2019-09-03 15:33 2.1K
netHg38.txt.gz 2019-09-03 15:33 22M
netMm10.sql 2019-09-03 15:33 2.1K
netMm10.txt.gz 2019-09-03 15:33 72M
netMm39.sql 2020-10-21 09:16 2.1K
netMm39.txt.gz 2020-10-21 09:16 72M
netNeoSch1.sql 2020-07-12 01:29 2.1K
netNeoSch1.txt.gz 2020-07-12 01:29 77M
refFlat.sql 2019-09-03 15:33 1.7K
refFlat.txt.gz 2019-09-03 15:33 503K
refGene.sql 2019-09-03 15:33 1.9K
refGene.txt.gz 2019-09-03 15:33 552K
refSeqAli.sql 2019-09-03 15:33 2.1K
refSeqAli.txt.gz 2019-09-03 15:33 563K
rhesusSNVs.sql 2020-05-19 14:27 1.3K
rhesusSNVs.txt.gz 2020-05-19 14:27 72
rmsk.sql 2019-09-03 15:33 1.9K
rmsk.txt.gz 2019-09-03 15:33 141M
seqNcbiRefSeq.sql 2019-09-03 15:34 1.5K
seqNcbiRefSeq.txt.gz 2019-09-03 15:34 1.3M
simpleRepeat.sql 2019-09-03 15:34 1.9K
simpleRepeat.txt.gz 2019-09-03 15:34 26M
tableDescriptions.sql 2024-11-23 02:04 1.4K
tableDescriptions.txt.gz 2024-11-23 02:04 6.7K
tableList.sql 2024-11-24 03:04 1.6K
tableList.txt.gz 2024-11-24 03:04 3.8K
tandemDups.sql 2019-09-03 15:34 1.8K
tandemDups.txt.gz 2019-09-03 15:34 30M
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 72K
ucscToINSDC.sql 2019-09-03 15:34 1.4K
ucscToINSDC.txt.gz 2019-09-03 15:34 25K
ucscToRefSeq.sql 2019-09-03 15:34 1.4K
ucscToRefSeq.txt.gz 2019-09-03 15:34 25K
windowmaskerSdust.sql 2019-09-03 15:34 1.5K
windowmaskerSdust.txt.gz 2019-09-03 15:34 146M
xenoRefFlat.sql 2019-09-03 15:35 1.7K
xenoRefFlat.txt.gz 2019-09-03 15:35 14M
xenoRefGene.sql 2019-09-03 15:35 1.9K
xenoRefGene.txt.gz 2019-09-03 15:35 16M
xenoRefSeqAli.sql 2019-09-03 15:35 2.1K
xenoRefSeqAli.txt.gz 2019-09-03 15:35 22M