This directory contains a dump of the UCSC genome annotation database for the
Jun 2013 (Macaca_fascicularis_5.0/macFas5) assembly of the crab-eating macaque genome
(macFas5, Washington University (WashU) GCA_000364345.1) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/776
http://www.ncbi.nlm.nih.gov/genome/assembly/704988
http://www.ncbi.nlm.nih.gov/bioproject/215851
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=macFas5
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/macFas5/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/macFas5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.soe.ucsc.edu/gbdb/
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 macFas5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql macFas5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Crab-eating macaque 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 2016-04-07 12:44 2.1K
all_est.txt.gz 2016-04-07 12:44 9.7M
augustusGene.sql 2016-04-07 12:44 1.9K
gold.sql 2016-04-07 12:44 1.7K
gold.txt.gz 2016-04-07 12:44 1.5M
grp.sql 2016-04-07 12:44 1.3K
grp.txt.gz 2016-04-07 12:44 206
augustusGene.txt.gz 2016-04-07 12:44 2.2M
chainHg19.sql 2016-04-07 12:44 1.7K
history.sql 2016-04-07 12:44 1.6K
history.txt.gz 2016-04-07 12:44 887
chainHg19.txt.gz 2016-04-07 12:44 15M
intronEst.sql 2016-04-07 12:44 2.1K
intronEst.txt.gz 2016-04-07 12:44 7.1M
chainHg19Link.sql 2016-04-07 12:44 1.5K
chainHg19Link.txt.gz 2016-04-07 12:45 177M
chainHg38.sql 2016-04-07 12:45 1.7K
chainHg38.txt.gz 2016-04-07 12:46 256M
chainHg38Link.sql 2016-04-07 12:47 1.5K
chainHg38Link.txt.gz 2016-04-07 12:48 783M
chainPapHam1.sql 2016-04-07 12:51 1.7K
chainPapHam1.txt.gz 2016-04-07 12:51 24M
chainPapHam1Link.sql 2016-04-07 12:51 1.5K
chainPapHam1Link.txt.gz 2016-04-07 12:51 84M
chainTarSyr2.sql 2016-04-07 12:51 1.7K
chainTarSyr2.txt.gz 2016-04-07 12:52 291M
chainTarSyr2Link.sql 2016-04-07 12:53 1.5K
chainTarSyr2Link.txt.gz 2016-04-07 12:54 1.2G
chromInfo.sql 2016-04-07 12:59 1.4K
chromInfo.txt.gz 2016-04-07 12:59 40K
cpgIslandExt.sql 2016-04-07 12:59 1.7K
cpgIslandExt.txt.gz 2016-04-07 12:59 607K
cpgIslandExtUnmasked.sql 2016-04-07 12:59 1.7K
cpgIslandExtUnmasked.txt.gz 2016-04-07 12:59 1.5M
cytoBandIdeo.sql 2016-04-07 12:59 1.5K
cytoBandIdeo.txt.gz 2016-04-07 12:59 38K
gc5BaseBw.sql 2016-04-07 12:59 1.3K
gc5BaseBw.txt.gz 2016-04-07 12:59 63
estOrientInfo.sql 2016-04-07 12:59 1.8K
estOrientInfo.txt.gz 2016-04-07 12:59 1.8M
genscan.sql 2016-04-07 12:59 1.7K
genscan.txt.gz 2016-04-07 12:59 2.9M
gap.sql 2016-04-07 12:59 1.6K
gap.txt.gz 2016-04-07 12:59 1.1M
microsat.sql 2016-04-07 12:59 1.5K
microsat.txt.gz 2016-04-07 12:59 373K
netHg19.sql 2016-04-07 12:59 2.1K
netHg19.txt.gz 2016-04-07 12:59 21M
netHg38.sql 2016-04-07 12:59 2.1K
netHg38.txt.gz 2016-04-07 12:59 22M
windowmaskerSdust.sql 2016-04-07 12:59 1.5K
windowmaskerSdust.txt.gz 2016-04-07 12:59 104M
netPapHam1.sql 2016-04-07 12:59 2.1K
netPapHam1.txt.gz 2016-04-07 12:59 19M
netTarSyr2.sql 2016-04-07 13:00 2.1K
netTarSyr2.txt.gz 2016-04-07 13:00 67M
rmsk.sql 2016-04-07 13:00 1.9K
rmsk.txt.gz 2016-04-07 13:00 135M
simpleRepeat.sql 2016-04-07 13:01 1.9K
simpleRepeat.txt.gz 2016-04-07 13:01 25M
chromAlias.sql 2018-02-04 08:05 1.4K
chromAlias.txt.gz 2018-02-04 08:05 82K
ucscToINSDC.sql 2018-02-04 08:05 1.4K
ucscToINSDC.txt.gz 2018-02-04 08:05 57K
ucscToRefSeq.sql 2018-02-04 08:05 1.4K
ucscToRefSeq.txt.gz 2018-02-04 08:05 60K
refSeqAli.sql 2020-03-01 07:36 2.1K
refSeqAli.txt.gz 2020-03-01 07:36 207K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.7M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 435K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 165K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.0M
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 10M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.6M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 5.3M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.1M
all_mrna.sql 2020-08-19 14:23 2.1K
all_mrna.txt.gz 2020-08-19 14:23 1.0M
mrnaOrientInfo.sql 2020-08-19 14:23 1.8K
mrnaOrientInfo.txt.gz 2020-08-19 14:23 258K
refGene.sql 2020-08-19 14:37 1.9K
refGene.txt.gz 2020-08-19 14:37 200K
refFlat.sql 2020-08-19 14:40 1.7K
refFlat.txt.gz 2020-08-19 14:40 187K
xenoRefGene.sql 2020-08-19 14:40 2.0K
xenoRefGene.txt.gz 2020-08-19 14:40 33M
xenoRefFlat.sql 2020-08-19 14:40 1.7K
xenoRefFlat.txt.gz 2020-08-19 14:40 30M
xenoRefSeqAli.sql 2020-08-19 14:40 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 14:40 32M
gbLoaded.sql 2020-08-19 14:53 1.6K
gbLoaded.txt.gz 2020-08-19 14:53 44K
ensGene.sql 2020-08-31 15:39 1.9K
ensGene.txt.gz 2020-08-31 15:39 3.2M
ensGtp.sql 2020-08-31 15:39 1.4K
ensGtp.txt.gz 2020-08-31 15:39 486K
ensemblToGeneName.sql 2020-08-31 15:39 1.4K
ensemblToGeneName.txt.gz 2020-08-31 15:39 249K
ensemblSource.sql 2020-08-31 16:00 1.4K
ensemblSource.txt.gz 2020-08-31 16:00 145K
ensPep.sql 2020-08-31 16:00 1.3K
ensPep.txt.gz 2020-08-31 16:00 7.4M
chainCalJac4.sql 2020-11-03 01:39 1.7K
chainCalJac4.txt.gz 2020-11-03 01:39 435M
chainCalJac4Link.sql 2020-11-03 01:51 1.6K
chainCalJac4Link.txt.gz 2020-11-03 01:51 1.3G
netCalJac4.sql 2020-11-03 01:54 2.1K
netCalJac4.txt.gz 2020-11-03 01:54 49M
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 68K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 7.6K
tableList.sql 2024-11-17 03:38 1.6K
tableList.txt.gz 2024-11-17 03:38 3.7K
bigFiles.sql 2024-11-17 03:38 1.4K
bigFiles.txt.gz 2024-11-17 03:38 94