This directory contains a dump of the UCSC genome annotation database for the
Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) assembly of the tarsier genome
(tarSyr2, Washington University) .
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/766
http://www.ncbi.nlm.nih.gov/assembly/784738
http://www.ncbi.nlm.nih.gov/bioproject/20339
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=tarSyr2
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.cse.ucsc.edu, then go to
the directory goldenPath/tarSyr2/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.cse.ucsc.edu/goldenPath/tarSyr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/tarSyr2/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.cse.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 tarSyr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql tarSyr2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Tarsier 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 -
nestedRepeats.sql 2015-04-02 12:52 1.9K
nestedRepeats.txt.gz 2015-04-02 12:52 18M
chromInfo.sql 2015-04-02 12:52 1.4K
chromInfo.txt.gz 2015-04-02 12:52 1.6M
cpgIslandExt.sql 2015-04-02 12:52 1.7K
cpgIslandExt.txt.gz 2015-04-02 12:52 872K
cpgIslandExtUnmasked.sql 2015-04-02 12:52 1.7K
cpgIslandExtUnmasked.txt.gz 2015-04-02 12:52 1.5M
genscan.sql 2015-04-02 12:52 1.7K
genscan.txt.gz 2015-04-02 12:52 3.5M
grp.sql 2015-04-02 12:52 1.3K
grp.txt.gz 2015-04-02 12:52 213
cytoBandIdeo.sql 2015-04-02 12:52 1.5K
cytoBandIdeo.txt.gz 2015-04-02 12:52 1.6M
history.sql 2015-04-02 12:52 1.6K
history.txt.gz 2015-04-02 12:52 2.0K
gap.sql 2015-04-02 12:52 1.6K
gap.txt.gz 2015-04-02 12:52 1.8M
rmsk.sql 2015-04-02 12:52 1.9K
rmsk.txt.gz 2015-04-02 12:52 161M
simpleRepeat.sql 2015-04-02 12:53 1.9K
simpleRepeat.txt.gz 2015-04-02 12:53 28M
gc5BaseBw.sql 2015-04-02 12:53 1.3K
gc5BaseBw.txt.gz 2015-04-02 12:53 66
genscanSubopt.sql 2015-04-02 12:53 1.6K
genscanSubopt.txt.gz 2015-04-02 12:53 7.7M
gold.sql 2015-04-02 12:53 1.7K
gold.txt.gz 2015-04-02 12:53 5.6M
ucscToINSDC.sql 2015-04-02 12:53 1.4K
ucscToINSDC.txt.gz 2015-04-02 12:53 2.4M
windowmaskerSdust.sql 2015-04-02 12:53 1.5K
windowmaskerSdust.txt.gz 2015-04-02 12:53 171M
chainCalJac3.sql 2015-05-25 10:38 1.7K
chainCalJac3.txt.gz 2015-05-25 10:38 252M
chainCalJac3Link.sql 2015-05-25 10:39 1.5K
chainCalJac3Link.txt.gz 2015-05-25 10:41 1.1G
chainHg38.sql 2015-05-25 10:45 1.7K
chainHg38.txt.gz 2015-05-25 10:46 619M
chainCanFam3.sql 2015-05-25 10:48 1.7K
chainCanFam3.txt.gz 2015-05-25 10:48 276M
chainHg38Link.sql 2015-05-25 10:49 1.5K
chainHg38Link.txt.gz 2015-05-25 10:51 1.8G
chainCanFam3Link.sql 2015-05-25 10:58 1.5K
chainCanFam3Link.txt.gz 2015-05-25 10:59 1.1G
chainGorGor3.sql 2015-05-25 11:04 1.7K
chainGorGor3.txt.gz 2015-05-25 11:05 240M
chainGorGor3Link.sql 2015-05-25 11:09 1.5K
chainGorGor3Link.txt.gz 2015-05-25 11:11 1.0G
chainMm10.sql 2015-05-25 11:15 1.7K
chainMm10.txt.gz 2015-05-25 11:15 86M
chainMm10Link.sql 2015-05-25 11:15 1.5K
chainMm10Link.txt.gz 2015-05-25 11:16 581M
chainNomLeu3.sql 2015-05-25 11:18 1.7K
chainNomLeu3.txt.gz 2015-05-25 11:18 265M
chainNomLeu3Link.sql 2015-05-25 11:19 1.5K
chainNomLeu3Link.txt.gz 2015-05-25 11:21 1.1G
chainOtoGar3.sql 2015-05-25 11:25 1.7K
chainOtoGar3.txt.gz 2015-05-25 11:28 2.8G
chainOtoGar3Link.sql 2015-05-25 11:36 1.5K
chainOtoGar3Link.txt.gz 2015-05-25 11:46 7.5G
chainPanTro4.sql 2015-05-25 12:17 1.7K
chainPanTro4.txt.gz 2015-05-25 12:17 289M
chainPanTro4Link.sql 2015-05-25 12:18 1.5K
chainPanTro4Link.txt.gz 2015-05-25 12:20 1.2G
chainPapAnu2.sql 2015-05-25 12:24 1.7K
chainPapAnu2.txt.gz 2015-05-25 12:24 123M
chainPapAnu2Link.sql 2015-05-25 12:25 1.5K
chainPapAnu2Link.txt.gz 2015-05-25 12:26 834M
chainPonAbe2.sql 2015-05-25 12:29 1.7K
chainPonAbe2.txt.gz 2015-05-25 12:29 325M
chainPonAbe2Link.sql 2015-05-25 12:30 1.5K
chainPonAbe2Link.txt.gz 2015-05-25 12:32 1.4G
chainRheMac3.sql 2015-05-25 12:37 1.7K
chainRheMac3.txt.gz 2015-05-25 12:38 253M
chainRheMac3Link.sql 2015-05-25 12:38 1.5K
chainRheMac3Link.txt.gz 2015-05-25 12:40 1.1G
chainSaiBol1.sql 2015-05-25 12:44 1.7K
chainSaiBol1.txt.gz 2015-05-25 12:44 198M
chainSaiBol1Link.sql 2015-05-25 12:45 1.5K
chainSaiBol1Link.txt.gz 2015-05-25 12:46 933M
chainTupBel1.sql 2015-05-25 12:50 1.7K
chainTupBel1.txt.gz 2015-05-25 12:50 461M
chainTupBel1Link.sql 2015-05-25 12:51 1.5K
chainTupBel1Link.txt.gz 2015-05-25 12:53 1.3G
extFile.sql 2015-05-25 12:58 1.4K
extFile.txt.gz 2015-05-25 12:58 81
multiz20way.sql 2015-05-25 12:58 1.5K
multiz20way.txt.gz 2015-05-25 12:59 392M
multiz20wayFrames.sql 2015-05-25 13:00 1.7K
multiz20wayFrames.txt.gz 2015-05-25 13:00 20M
multiz20waySummary.sql 2015-05-25 13:00 1.6K
multiz20waySummary.txt.gz 2015-05-25 13:00 7.4M
netOtoGar3.sql 2015-05-25 13:00 2.1K
netOtoGar3.txt.gz 2015-05-25 13:00 81M
netCalJac3.sql 2015-05-25 13:00 2.1K
netCalJac3.txt.gz 2015-05-25 13:01 69M
netPanTro4.sql 2015-05-25 13:01 2.1K
netPanTro4.txt.gz 2015-05-25 13:01 64M
netCanFam3.sql 2015-05-25 13:01 2.1K
netCanFam3.txt.gz 2015-05-25 13:01 82M
netPapAnu2.sql 2015-05-25 13:02 2.1K
netPapAnu2.txt.gz 2015-05-25 13:02 67M
netGorGor3.sql 2015-05-25 13:02 2.1K
netGorGor3.txt.gz 2015-05-25 13:02 64M
netSaiBol1.sql 2015-05-25 13:02 2.1K
netSaiBol1.txt.gz 2015-05-25 13:02 66M
netHg38.sql 2015-05-25 13:03 2.1K
netHg38.txt.gz 2015-05-25 13:03 64M
netPonAbe2.sql 2015-05-25 13:03 2.1K
netPonAbe2.txt.gz 2015-05-25 13:03 66M
netTupBel1.sql 2015-05-25 13:04 2.1K
netTupBel1.txt.gz 2015-05-25 13:04 70M
netMm10.sql 2015-05-25 13:04 2.1K
netMm10.txt.gz 2015-05-25 13:04 71M
netRheMac3.sql 2015-05-25 13:05 2.1K
netRheMac3.txt.gz 2015-05-25 13:05 67M
netNomLeu3.sql 2015-05-25 13:05 2.1K
netNomLeu3.txt.gz 2015-05-25 13:05 66M
phastCons20way.sql 2015-05-25 13:05 1.8K
phastCons20way.txt.gz 2015-05-25 13:05 82M
phastConsElements20way.sql 2015-05-25 13:06 1.6K
phastConsElements20way.txt.gz 2015-05-25 13:06 6.7M
phyloP20way.sql 2015-05-25 13:06 1.8K
phyloP20way.txt.gz 2015-05-25 13:06 96M
chainPanPan1.sql 2015-07-06 11:22 1.7K
chainPanPan1.txt.gz 2015-07-06 11:22 121M
chainPanPan1Link.sql 2015-07-06 11:22 1.5K
chainPanPan1Link.txt.gz 2015-07-06 11:23 795M
netPanPan1.sql 2015-07-06 11:27 2.1K
netPanPan1.txt.gz 2015-07-06 11:27 65M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.2M
microsat.sql 2015-08-24 02:25 1.5K
microsat.txt.gz 2015-08-24 02:25 755K
chainMicMur2Link.sql 2016-02-15 01:41 1.5K
chainMicMur2Link.txt.gz 2016-02-15 01:42 1.0G
chainMicMur2.sql 2016-02-15 01:46 1.7K
chainMicMur2.txt.gz 2016-02-15 01:47 217M
netMicMur2.sql 2016-02-15 01:47 2.1K
netMicMur2.txt.gz 2016-02-15 01:47 68M
chainMacFas5.sql 2016-04-10 03:34 1.7K
chainMacFas5.txt.gz 2016-04-10 03:34 276M
chainMacFas5Link.sql 2016-04-10 03:35 1.5K
chainMacFas5Link.txt.gz 2016-04-10 03:36 1.2G
netMacFas5.sql 2016-04-10 03:41 2.1K
netMacFas5.txt.gz 2016-04-10 03:42 66M
all_mrna.sql 2016-09-18 11:23 2.1K
all_mrna.txt.gz 2016-09-18 11:23 33
mrnaOrientInfo.sql 2016-09-18 11:23 1.8K
mrnaOrientInfo.txt.gz 2016-09-18 11:23 39
chainChlSab2.sql 2016-10-30 10:11 1.7K
chainChlSab2.txt.gz 2016-10-30 10:12 270M
chainChlSab2Link.sql 2016-10-30 10:13 1.5K
chainChlSab2Link.txt.gz 2016-10-30 10:14 1.2G
netChlSab2.sql 2016-10-30 10:18 2.1K
netChlSab2.txt.gz 2016-10-30 10:19 66M
netNasLar1.sql 2017-03-13 13:55 2.1K
netNasLar1.txt.gz 2017-03-13 13:57 68M
chainNasLar1.sql 2017-03-13 13:59 1.7K
chainNasLar1.txt.gz 2017-03-13 14:02 223M
chainNasLar1Link.sql 2017-03-13 14:09 1.5K
chainNasLar1Link.txt.gz 2017-03-13 14:20 953M
chainRn6.sql 2017-03-28 07:28 1.7K
chainRn6.txt.gz 2017-03-28 07:31 348M
netRn6.sql 2017-03-28 07:44 2.1K
netRn6.txt.gz 2017-03-28 07:46 82M
chainRn6Link.sql 2017-03-28 07:51 1.5K
chainRn6Link.txt.gz 2017-03-28 08:14 1.7G
chromAlias.sql 2018-02-04 09:36 1.4K
chromAlias.txt.gz 2018-02-04 09:36 3.3M
ucscToRefSeq.sql 2018-02-18 08:51 1.4K
ucscToRefSeq.txt.gz 2018-02-18 08:51 2.4M
chainRhiRox1.sql 2019-02-17 03:27 1.7K
chainRhiRox1.txt.gz 2019-02-17 03:27 305M
chainRhiRox1Link.sql 2019-02-17 03:28 1.5K
chainRhiRox1Link.txt.gz 2019-02-17 03:29 1.2G
netRhiRox1.sql 2019-02-17 03:34 2.1K
netRhiRox1.txt.gz 2019-02-17 03:34 68M
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:29 90
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:29 2.3M
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 217K
ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 325
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.0M
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 7.3M
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.3M
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 2.7M
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 546K
xenoRefGene.sql 2020-08-20 13:36 2.0K
xenoRefGene.txt.gz 2020-08-20 13:36 33M
xenoRefFlat.sql 2020-08-20 13:42 1.7K
xenoRefFlat.txt.gz 2020-08-20 13:42 30M
xenoRefSeqAli.sql 2020-08-20 13:42 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 13:42 35M
gbLoaded.sql 2020-08-20 13:48 1.6K
gbLoaded.txt.gz 2020-08-20 13:48 19K
chainMm39.sql 2020-11-24 02:14 1.7K
chainMm39.txt.gz 2020-11-24 02:14 59M
chainMm39Link.sql 2020-11-24 02:18 1.6K
chainMm39Link.txt.gz 2020-11-24 02:18 484M
netMm39.sql 2020-11-24 02:23 2.1K
netMm39.txt.gz 2020-11-24 02:23 71M
ensGene.sql 2021-05-25 14:50 1.9K
ensGene.txt.gz 2021-05-25 14:50 2.3M
ensGtp.sql 2021-05-25 14:50 1.4K
ensGtp.txt.gz 2021-05-25 14:50 379K
ensemblToGeneName.sql 2021-05-25 14:50 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:50 202K
ensemblSource.sql 2021-05-25 14:54 1.4K
ensemblSource.txt.gz 2021-05-25 14:54 110K
ensPep.sql 2021-05-25 14:54 1.3K
ensPep.txt.gz 2021-05-25 14:54 9.2M
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 70K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 9.1K
tableList.sql 2024-11-24 03:25 1.6K
tableList.txt.gz 2024-11-24 03:25 6.0K
bigFiles.sql 2024-11-24 03:25 1.4K
bigFiles.txt.gz 2024-11-24 03:25 95