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