This directory contains a dump of the UCSC genome annotation database for the
May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4) assembly of the marmoset genome
(calJac4, McDonnell Genome Institute at Washington University) .
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/442
https://www.ncbi.nlm.nih.gov/genome/assembly/7157801
https://www.ncbi.nlm.nih.gov/bioproject/566173
https://www.ncbi.nlm.nih.gov/biosample/SAMN12783337
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=calJac4
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/calJac4/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/calJac4/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/calJac4/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac4/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 calJac4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calJac4 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Marmoset 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 -
gold.sql 2020-09-02 09:56 1.7K
gold.txt.gz 2020-09-02 09:56 21K
gap.sql 2020-09-02 09:56 1.6K
gap.txt.gz 2020-09-02 09:56 6.3K
cpgIslandExtUnmasked.sql 2020-09-02 10:12 1.7K
cpgIslandExtUnmasked.txt.gz 2020-09-02 10:12 810K
simpleRepeat.sql 2020-09-02 12:20 1.9K
simpleRepeat.txt.gz 2020-09-02 12:20 22M
gc5BaseBw.sql 2020-09-02 13:12 1.3K
gc5BaseBw.txt.gz 2020-09-02 13:12 66
grp.sql 2020-09-02 13:12 1.4K
grp.txt.gz 2020-09-02 13:12 213
cytoBandIdeo.sql 2020-09-02 13:52 1.5K
cytoBandIdeo.txt.gz 2020-09-02 13:52 6.4K
chromInfo.sql 2020-09-02 16:33 1.4K
chromInfo.txt.gz 2020-09-02 16:33 6.8K
rmsk.sql 2020-09-02 16:36 1.9K
rmsk.txt.gz 2020-09-02 16:36 132M
nestedRepeats.sql 2020-09-02 16:38 2.0K
nestedRepeats.txt.gz 2020-09-02 16:38 16M
microsat.sql 2020-09-02 17:30 1.5K
microsat.txt.gz 2020-09-02 17:30 447K
windowmaskerSdust.sql 2020-09-02 19:26 1.5K
windowmaskerSdust.txt.gz 2020-09-02 19:26 138M
cpgIslandExt.sql 2020-09-03 10:57 1.7K
cpgIslandExt.txt.gz 2020-09-03 10:57 597K
chromAlias.sql 2020-09-03 11:38 1.4K
chromAlias.txt.gz 2020-09-03 11:38 16K
ucscToINSDC.sql 2020-09-04 01:39 1.4K
ucscToINSDC.txt.gz 2020-09-04 01:39 8.8K
ucscToRefSeq.sql 2020-09-04 01:39 1.5K
ucscToRefSeq.txt.gz 2020-09-04 01:39 8.5K
chainMm10.sql 2020-09-04 11:25 1.7K
chainMm10.txt.gz 2020-09-04 11:25 67M
chainMm10Link.sql 2020-09-04 11:29 1.6K
chainMm10Link.txt.gz 2020-09-04 11:29 504M
netMm10.sql 2020-09-04 11:32 2.1K
netMm10.txt.gz 2020-09-04 11:32 68M
chainHg38.sql 2020-09-04 11:53 1.7K
chainHg38.txt.gz 2020-09-04 11:53 536M
chainHg38Link.sql 2020-09-04 12:07 1.6K
chainHg38Link.txt.gz 2020-09-04 12:07 1.6G
netHg38.sql 2020-09-04 12:10 2.1K
netHg38.txt.gz 2020-09-04 12:10 43M
augustusGene.sql 2020-09-04 13:18 2.0K
augustusGene.txt.gz 2020-09-04 13:18 2.4M
chainMm39.sql 2020-09-04 23:44 1.7K
chainMm39.txt.gz 2020-09-04 23:44 78M
chainMm39Link.sql 2020-09-04 23:48 1.6K
chainMm39Link.txt.gz 2020-09-04 23:48 527M
netMm39.sql 2020-09-04 23:51 2.1K
netMm39.txt.gz 2020-09-04 23:51 68M
crisprAllTargets.sql 2020-09-10 14:46 1.3K
crisprAllTargets.txt.gz 2020-09-10 14:46 69
genscan.sql 2020-09-17 11:33 1.7K
genscan.txt.gz 2020-09-17 11:33 3.0M
all_mrna.sql 2020-09-21 09:15 2.1K
all_mrna.txt.gz 2020-09-21 09:15 73K
xenoMrna.sql 2020-09-21 09:16 2.1K
xenoMrna.txt.gz 2020-09-21 09:16 252M
refGene.sql 2020-09-21 09:50 1.9K
refGene.txt.gz 2020-09-21 09:50 21K
refFlat.sql 2020-09-21 09:50 1.7K
refFlat.txt.gz 2020-09-21 09:50 19K
xenoRefGene.sql 2020-09-21 09:50 2.0K
xenoRefGene.txt.gz 2020-09-21 09:50 12M
xenoRefFlat.sql 2020-09-21 09:50 1.7K
xenoRefFlat.txt.gz 2020-09-21 09:50 11M
refSeqAli.sql 2020-09-21 09:50 2.1K
refSeqAli.txt.gz 2020-09-21 09:50 22K
xenoRefSeqAli.sql 2020-09-21 09:50 2.1K
xenoRefSeqAli.txt.gz 2020-09-21 09:50 24M
estOrientInfo.sql 2020-09-21 09:52 1.8K
estOrientInfo.txt.gz 2020-09-21 09:52 3.0M
intronEst.sql 2020-09-21 09:52 2.1K
intronEst.txt.gz 2020-09-21 09:52 8.0M
all_est.sql 2020-09-21 09:52 2.1K
all_est.txt.gz 2020-09-21 09:52 9.6M
mrnaOrientInfo.sql 2020-09-21 09:53 1.8K
mrnaOrientInfo.txt.gz 2020-09-21 09:53 25K
extFile.sql 2020-10-01 14:16 1.4K
extFile.txt.gz 2020-10-01 14:16 105
ncbiRefSeq.sql 2020-10-27 12:26 2.0K
ncbiRefSeq.txt.gz 2020-10-27 12:26 4.6M
ncbiRefSeqCurated.sql 2020-10-27 12:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-10-27 12:26 20K
ncbiRefSeqPredicted.sql 2020-10-27 12:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-10-27 12:26 4.6M
ncbiRefSeqLink.sql 2020-10-27 12:26 2.0K
ncbiRefSeqLink.txt.gz 2020-10-27 12:26 2.6M
ncbiRefSeqPsl.sql 2020-10-27 12:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-10-27 12:26 7.1M
ncbiRefSeqOther.sql 2020-10-28 01:39 1.3K
ncbiRefSeqOther.txt.gz 2020-10-28 01:39 75
ncbiRefSeqCds.sql 2020-10-28 01:39 1.4K
ncbiRefSeqCds.txt.gz 2020-10-28 01:39 594K
ncbiRefSeqPepTable.sql 2020-10-28 01:39 1.4K
ncbiRefSeqPepTable.txt.gz 2020-10-28 01:39 13M
extNcbiRefSeq.sql 2020-10-28 01:39 1.5K
extNcbiRefSeq.txt.gz 2020-10-28 01:39 91
seqNcbiRefSeq.sql 2020-10-28 01:39 1.6K
seqNcbiRefSeq.txt.gz 2020-10-28 01:39 1.6M
chainMacFas5.sql 2020-11-03 00:02 1.7K
chainMacFas5.txt.gz 2020-11-03 00:02 432M
chainMacFas5Link.sql 2020-11-03 00:15 1.6K
chainMacFas5Link.txt.gz 2020-11-03 00:15 1.3G
netMacFas5.sql 2020-11-03 00:18 2.1K
netMacFas5.txt.gz 2020-11-03 00:18 45M
history.sql 2020-11-04 07:48 1.6K
history.txt.gz 2020-11-04 07:48 1.4K
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 32K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 1.1K
tableDescriptions.sql 2024-12-07 02:04 1.5K
tableDescriptions.txt.gz 2024-12-07 02:04 6.1K
tableList.sql 2024-12-08 03:04 1.6K
tableList.txt.gz 2024-12-08 03:04 3.5K
bigFiles.sql 2024-12-08 03:04 1.4K
bigFiles.txt.gz 2024-12-08 03:04 119