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 -
all_mrna.txt.gz 2016-09-18 11:23 33
mrnaOrientInfo.txt.gz 2016-09-18 11:23 39
gc5BaseBw.txt.gz 2015-04-02 12:53 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 75
extFile.txt.gz 2015-05-25 12:58 81
extNcbiRefSeq.txt.gz 2020-05-10 03:29 90
bigFiles.txt.gz 2024-11-24 03:25 95
grp.txt.gz 2015-04-02 12:52 213
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 325
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
gc5BaseBw.sql 2015-04-02 12:53 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ensPep.sql 2021-05-25 14:54 1.3K
grp.sql 2015-04-02 12:52 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ensemblSource.sql 2021-05-25 14:54 1.4K
chromInfo.sql 2015-04-02 12:52 1.4K
bigFiles.sql 2024-11-24 03:25 1.4K
ensemblToGeneName.sql 2021-05-25 14:50 1.4K
extFile.sql 2015-05-25 12:58 1.4K
chromAlias.sql 2018-02-04 09:36 1.4K
ucscToINSDC.sql 2015-04-02 12:53 1.4K
ucscToRefSeq.sql 2018-02-18 08:51 1.4K
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
ensGtp.sql 2021-05-25 14:50 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.5K
microsat.sql 2015-08-24 02:25 1.5K
windowmaskerSdust.sql 2015-04-02 12:53 1.5K
cytoBandIdeo.sql 2015-04-02 12:52 1.5K
multiz20way.sql 2015-05-25 12:58 1.5K
chainRn6Link.sql 2017-03-28 07:51 1.5K
chainHg38Link.sql 2015-05-25 10:49 1.5K
chainMm10Link.sql 2015-05-25 11:15 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
chainCalJac3Link.sql 2015-05-25 10:39 1.5K
chainCanFam3Link.sql 2015-05-25 10:58 1.5K
chainChlSab2Link.sql 2016-10-30 10:13 1.5K
chainGorGor3Link.sql 2015-05-25 11:09 1.5K
chainMacFas5Link.sql 2016-04-10 03:35 1.5K
chainMicMur2Link.sql 2016-02-15 01:41 1.5K
chainNasLar1Link.sql 2017-03-13 14:09 1.5K
chainNomLeu3Link.sql 2015-05-25 11:19 1.5K
chainOtoGar3Link.sql 2015-05-25 11:36 1.5K
chainPanPan1Link.sql 2015-07-06 11:22 1.5K
chainPanTro4Link.sql 2015-05-25 12:18 1.5K
chainPapAnu2Link.sql 2015-05-25 12:25 1.5K
chainPonAbe2Link.sql 2015-05-25 12:30 1.5K
chainRheMac3Link.sql 2015-05-25 12:38 1.5K
chainRhiRox1Link.sql 2019-02-17 03:28 1.5K
chainSaiBol1Link.sql 2015-05-25 12:45 1.5K
chainTupBel1Link.sql 2015-05-25 12:51 1.5K
chainMm39Link.sql 2020-11-24 02:18 1.6K
phastConsElements20way.sql 2015-05-25 13:06 1.6K
genscanSubopt.sql 2015-04-02 12:53 1.6K
history.sql 2015-04-02 12:52 1.6K
multiz20waySummary.sql 2015-05-25 13:00 1.6K
tableList.sql 2024-11-24 03:25 1.6K
gap.sql 2015-04-02 12:52 1.6K
gbLoaded.sql 2020-08-20 13:48 1.6K
gold.sql 2015-04-02 12:53 1.7K
genscan.sql 2015-04-02 12:52 1.7K
cpgIslandExt.sql 2015-04-02 12:52 1.7K
chainRn6.sql 2017-03-28 07:28 1.7K
chainHg38.sql 2015-05-25 10:45 1.7K
chainMm10.sql 2015-05-25 11:15 1.7K
chainCalJac3.sql 2015-05-25 10:38 1.7K
chainCanFam3.sql 2015-05-25 10:48 1.7K
chainChlSab2.sql 2016-10-30 10:11 1.7K
chainGorGor3.sql 2015-05-25 11:04 1.7K
chainMacFas5.sql 2016-04-10 03:34 1.7K
chainMicMur2.sql 2016-02-15 01:46 1.7K
chainNasLar1.sql 2017-03-13 13:59 1.7K
chainNomLeu3.sql 2015-05-25 11:18 1.7K
chainOtoGar3.sql 2015-05-25 11:25 1.7K
chainPanPan1.sql 2015-07-06 11:22 1.7K
chainPanTro4.sql 2015-05-25 12:17 1.7K
chainPapAnu2.sql 2015-05-25 12:24 1.7K
chainPonAbe2.sql 2015-05-25 12:29 1.7K
chainRheMac3.sql 2015-05-25 12:37 1.7K
chainRhiRox1.sql 2019-02-17 03:27 1.7K
chainSaiBol1.sql 2015-05-25 12:44 1.7K
chainTupBel1.sql 2015-05-25 12:50 1.7K
cpgIslandExtUnmasked.sql 2015-04-02 12:52 1.7K
chainMm39.sql 2020-11-24 02:14 1.7K
multiz20wayFrames.sql 2015-05-25 13:00 1.7K
xenoRefFlat.sql 2020-08-20 13:42 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
phyloP20way.sql 2015-05-25 13:06 1.8K
mrnaOrientInfo.sql 2016-09-18 11:23 1.8K
phastCons20way.sql 2015-05-25 13:05 1.8K
rmsk.sql 2015-04-02 12:52 1.9K
simpleRepeat.sql 2015-04-02 12:53 1.9K
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
nestedRepeats.sql 2015-04-02 12:52 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
ensGene.sql 2021-05-25 14:50 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:29 2.0K
xenoRefGene.sql 2020-08-20 13:36 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
history.txt.gz 2015-04-02 12:52 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netRn6.sql 2017-03-28 07:44 2.1K
netHg38.sql 2015-05-25 13:03 2.1K
netMm10.sql 2015-05-25 13:04 2.1K
netCalJac3.sql 2015-05-25 13:00 2.1K
netCanFam3.sql 2015-05-25 13:01 2.1K
netChlSab2.sql 2016-10-30 10:18 2.1K
netGorGor3.sql 2015-05-25 13:02 2.1K
netMacFas5.sql 2016-04-10 03:41 2.1K
netMicMur2.sql 2016-02-15 01:47 2.1K
netNasLar1.sql 2017-03-13 13:55 2.1K
netNomLeu3.sql 2015-05-25 13:05 2.1K
netOtoGar3.sql 2015-05-25 13:00 2.1K
netPanPan1.sql 2015-07-06 11:27 2.1K
netPanTro4.sql 2015-05-25 13:01 2.1K
netPapAnu2.sql 2015-05-25 13:02 2.1K
netPonAbe2.sql 2015-05-25 13:03 2.1K
netRheMac3.sql 2015-05-25 13:05 2.1K
netRhiRox1.sql 2019-02-17 03:34 2.1K
netSaiBol1.sql 2015-05-25 13:02 2.1K
netTupBel1.sql 2015-05-25 13:04 2.1K
all_mrna.sql 2016-09-18 11:23 2.1K
netMm39.sql 2020-11-24 02:23 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
xenoRefSeqAli.sql 2020-08-20 13:42 2.1K
tableList.txt.gz 2024-11-24 03:25 6.0K
tableDescriptions.txt.gz 2024-11-23 02:03 9.1K
gbLoaded.txt.gz 2020-08-20 13:48 19K
trackDb.txt.gz 2024-01-31 15:13 70K
ensemblSource.txt.gz 2021-05-25 14:54 110K
ensemblToGeneName.txt.gz 2021-05-25 14:50 202K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 217K
ensGtp.txt.gz 2021-05-25 14:50 379K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 546K
microsat.txt.gz 2015-08-24 02:25 755K
cpgIslandExt.txt.gz 2015-04-02 12:52 872K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 1.0M
cpgIslandExtUnmasked.txt.gz 2015-04-02 12:52 1.5M
chromInfo.txt.gz 2015-04-02 12:52 1.6M
cytoBandIdeo.txt.gz 2015-04-02 12:52 1.6M
gap.txt.gz 2015-04-02 12:52 1.8M
augustusGene.txt.gz 2015-07-26 17:28 2.2M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.3M
ncbiRefSeq.txt.gz 2020-05-10 03:29 2.3M
ensGene.txt.gz 2021-05-25 14:50 2.3M
ucscToRefSeq.txt.gz 2018-02-18 08:51 2.4M
ucscToINSDC.txt.gz 2015-04-02 12:53 2.4M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 2.7M
chromAlias.txt.gz 2018-02-04 09:36 3.3M
genscan.txt.gz 2015-04-02 12:52 3.5M
gold.txt.gz 2015-04-02 12:53 5.6M
phastConsElements20way.txt.gz 2015-05-25 13:06 6.7M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 7.3M
multiz20waySummary.txt.gz 2015-05-25 13:00 7.4M
genscanSubopt.txt.gz 2015-04-02 12:53 7.7M
ensPep.txt.gz 2021-05-25 14:54 9.2M
nestedRepeats.txt.gz 2015-04-02 12:52 18M
multiz20wayFrames.txt.gz 2015-05-25 13:00 20M
simpleRepeat.txt.gz 2015-04-02 12:53 28M
xenoRefFlat.txt.gz 2020-08-20 13:42 30M
xenoRefGene.txt.gz 2020-08-20 13:36 33M
xenoRefSeqAli.txt.gz 2020-08-20 13:42 35M
chainMm39.txt.gz 2020-11-24 02:14 59M
netGorGor3.txt.gz 2015-05-25 13:02 64M
netPanTro4.txt.gz 2015-05-25 13:01 64M
netHg38.txt.gz 2015-05-25 13:03 64M
netPanPan1.txt.gz 2015-07-06 11:27 65M
netNomLeu3.txt.gz 2015-05-25 13:05 66M
netSaiBol1.txt.gz 2015-05-25 13:02 66M
netChlSab2.txt.gz 2016-10-30 10:19 66M
netMacFas5.txt.gz 2016-04-10 03:42 66M
netPonAbe2.txt.gz 2015-05-25 13:03 66M
netRheMac3.txt.gz 2015-05-25 13:05 67M
netPapAnu2.txt.gz 2015-05-25 13:02 67M
netMicMur2.txt.gz 2016-02-15 01:47 68M
netRhiRox1.txt.gz 2019-02-17 03:34 68M
netNasLar1.txt.gz 2017-03-13 13:57 68M
netCalJac3.txt.gz 2015-05-25 13:01 69M
netTupBel1.txt.gz 2015-05-25 13:04 70M
netMm10.txt.gz 2015-05-25 13:04 71M
netMm39.txt.gz 2020-11-24 02:23 71M
netOtoGar3.txt.gz 2015-05-25 13:00 81M
netCanFam3.txt.gz 2015-05-25 13:01 82M
phastCons20way.txt.gz 2015-05-25 13:05 82M
netRn6.txt.gz 2017-03-28 07:46 82M
chainMm10.txt.gz 2015-05-25 11:15 86M
phyloP20way.txt.gz 2015-05-25 13:06 96M
chainPanPan1.txt.gz 2015-07-06 11:22 121M
chainPapAnu2.txt.gz 2015-05-25 12:24 123M
rmsk.txt.gz 2015-04-02 12:52 161M
windowmaskerSdust.txt.gz 2015-04-02 12:53 171M
chainSaiBol1.txt.gz 2015-05-25 12:44 198M
chainMicMur2.txt.gz 2016-02-15 01:47 217M
chainNasLar1.txt.gz 2017-03-13 14:02 223M
chainGorGor3.txt.gz 2015-05-25 11:05 240M
chainCalJac3.txt.gz 2015-05-25 10:38 252M
chainRheMac3.txt.gz 2015-05-25 12:38 253M
chainNomLeu3.txt.gz 2015-05-25 11:18 265M
chainChlSab2.txt.gz 2016-10-30 10:12 270M
chainMacFas5.txt.gz 2016-04-10 03:34 276M
chainCanFam3.txt.gz 2015-05-25 10:48 276M
chainPanTro4.txt.gz 2015-05-25 12:17 289M
chainRhiRox1.txt.gz 2019-02-17 03:27 305M
chainPonAbe2.txt.gz 2015-05-25 12:29 325M
chainRn6.txt.gz 2017-03-28 07:31 348M
multiz20way.txt.gz 2015-05-25 12:59 392M
chainTupBel1.txt.gz 2015-05-25 12:50 461M
chainMm39Link.txt.gz 2020-11-24 02:18 484M
chainMm10Link.txt.gz 2015-05-25 11:16 581M
chainHg38.txt.gz 2015-05-25 10:46 619M
chainPanPan1Link.txt.gz 2015-07-06 11:23 795M
chainPapAnu2Link.txt.gz 2015-05-25 12:26 834M
chainSaiBol1Link.txt.gz 2015-05-25 12:46 933M
chainNasLar1Link.txt.gz 2017-03-13 14:20 953M
chainMicMur2Link.txt.gz 2016-02-15 01:42 1.0G
chainGorGor3Link.txt.gz 2015-05-25 11:11 1.0G
chainCanFam3Link.txt.gz 2015-05-25 10:59 1.1G
chainRheMac3Link.txt.gz 2015-05-25 12:40 1.1G
chainCalJac3Link.txt.gz 2015-05-25 10:41 1.1G
chainNomLeu3Link.txt.gz 2015-05-25 11:21 1.1G
chainChlSab2Link.txt.gz 2016-10-30 10:14 1.2G
chainRhiRox1Link.txt.gz 2019-02-17 03:29 1.2G
chainMacFas5Link.txt.gz 2016-04-10 03:36 1.2G
chainPanTro4Link.txt.gz 2015-05-25 12:20 1.2G
chainTupBel1Link.txt.gz 2015-05-25 12:53 1.3G
chainPonAbe2Link.txt.gz 2015-05-25 12:32 1.4G
chainRn6Link.txt.gz 2017-03-28 08:14 1.7G
chainHg38Link.txt.gz 2015-05-25 10:51 1.8G
chainOtoGar3.txt.gz 2015-05-25 11:28 2.8G
chainOtoGar3Link.txt.gz 2015-05-25 11:46 7.5G