This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of the chimp genome
(panTro3, CGSC 2.1.3 (GCA_000001515.3)) from the
Chimp Genome Sequencing Consortium.  The annotations were generated
by UCSC and collaborators worldwide.

This assembly was produced by the Chimpanzee Sequencing and Analysis Consortium.

For more information on the chimp genome, see the project website:
http://genome.wustl.edu/genomes/view/pan_troglodytes/

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=panTro3
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/panTro3/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/panTro3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/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 panTro3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'


##############################################################################

The chimpanzee sequence is made freely available before scientific
publication 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
   particular genes and regions 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.

      Name                                 Last modified      Size  Description
Parent Directory - gold.sql 2011-02-25 17:09 1.6K gold.txt.gz 2011-02-25 17:09 3.0M chromInfo.sql 2011-02-25 17:10 1.3K chromInfo.txt.gz 2011-02-25 17:10 138K nestedRepeats.sql 2011-02-25 17:10 1.9K nestedRepeats.txt.gz 2011-02-25 17:10 18M ctgPos2.sql 2011-02-25 17:10 1.5K ctgPos2.txt.gz 2011-02-25 17:10 2.5M history.sql 2011-02-25 17:11 1.5K history.txt.gz 2011-02-25 17:11 147 chainHg19.sql 2011-02-25 17:11 1.6K chainHg19.txt.gz 2011-02-25 17:11 28M simpleRepeat.sql 2011-02-25 17:13 1.9K simpleRepeat.txt.gz 2011-02-25 17:13 26M cpgIslandExt.sql 2011-02-25 17:14 1.6K cpgIslandExt.txt.gz 2011-02-25 17:14 627K netHg19.sql 2011-02-25 17:17 2.0K netHg19.txt.gz 2011-02-25 17:18 10M chainHg19Link.sql 2011-02-25 17:18 1.5K chainHg19Link.txt.gz 2011-02-25 17:19 124M gap.sql 2011-02-25 17:24 1.5K gap.txt.gz 2011-02-25 17:24 2.3M rmsk.sql 2011-02-25 17:28 1.8K rmsk.txt.gz 2011-02-25 17:29 137M gc5BaseBw.sql 2011-02-25 17:35 1.2K gc5BaseBw.txt.gz 2011-02-25 17:35 63 chainDanRer7.sql 2011-03-15 09:00 1.6K chainDanRer7.txt.gz 2011-03-15 09:02 160M chainDanRer7Link.sql 2011-03-15 09:08 1.5K chainDanRer7Link.txt.gz 2011-03-15 09:15 524M netDanRer7.sql 2011-03-15 09:36 2.0K netDanRer7.txt.gz 2011-03-15 09:36 8.1M chainGalGal3Link.sql 2011-05-03 13:23 1.5K chainGalGal3Link.txt.gz 2011-05-03 13:25 114M chainPonAbe2.sql 2011-05-03 13:29 1.6K chainPonAbe2.txt.gz 2011-05-03 13:29 26M chainPonAbe2Link.sql 2011-05-03 13:30 1.5K chainPonAbe2Link.txt.gz 2011-05-03 13:32 175M netEquCab2.sql 2011-05-03 13:39 2.0K netEquCab2.txt.gz 2011-05-03 13:41 70M chainGalGal3.sql 2011-05-03 13:43 1.6K chainGalGal3.txt.gz 2011-05-03 13:44 21M netGalGal3.sql 2011-05-03 13:44 2.0K netGalGal3.txt.gz 2011-05-03 13:45 12M chainEquCab2Link.sql 2011-05-03 13:45 1.5K chainEquCab2Link.txt.gz 2011-05-03 13:59 1.0G chainEquCab2.sql 2011-05-03 14:38 1.6K chainEquCab2.txt.gz 2011-05-03 14:41 258M netPonAbe2.sql 2011-05-03 14:49 2.0K netPonAbe2.txt.gz 2011-05-03 14:50 20M chainMm9Link.sql 2011-05-24 00:21 1.5K chainMm9Link.txt.gz 2011-05-24 00:24 520M netRheMac2.sql 2011-05-24 00:30 2.0K netRheMac2.txt.gz 2011-05-24 00:30 26M netMm9.sql 2011-05-24 00:31 2.0K netMm9.txt.gz 2011-05-24 00:32 73M netCalJac3.sql 2011-05-24 00:32 2.0K netCalJac3.txt.gz 2011-05-24 00:33 45M chainMm9.sql 2011-05-24 00:34 1.6K chainMm9.txt.gz 2011-05-24 00:34 67M chainCalJac3.sql 2011-05-24 00:35 1.6K chainCalJac3.txt.gz 2011-05-24 00:35 15M chainCalJac3Link.sql 2011-05-24 00:35 1.5K chainCalJac3Link.txt.gz 2011-05-24 00:37 235M chainRheMac2.sql 2011-05-24 00:40 1.6K chainRheMac2.txt.gz 2011-05-24 00:40 11M chainRheMac2Link.sql 2011-05-24 00:40 1.5K chainRheMac2Link.txt.gz 2011-05-24 00:41 162M chainCanFam2Link.sql 2011-05-30 01:12 1.5K chainCanFam2Link.txt.gz 2011-05-30 01:13 524M chainCanFam2.sql 2011-05-30 01:18 1.6K chainCanFam2.txt.gz 2011-05-30 01:19 43M netCanFam2.sql 2011-05-30 01:19 2.0K netCanFam2.txt.gz 2011-05-30 01:20 77M nscanGene.sql 2011-06-26 14:55 1.9K nscanGene.txt.gz 2011-06-26 14:55 2.2M nscanPep.sql 2011-06-26 14:55 1.3K nscanPep.txt.gz 2011-06-26 14:55 6.1M phyloP12wayPrimate.sql 2011-08-21 03:56 1.7K phyloP12wayPrimate.txt.gz 2011-08-21 03:56 82M phastConsElements12way.sql 2011-08-21 03:56 1.5K phastConsElements12way.txt.gz 2011-08-21 03:56 14M phastCons12wayPrimate.sql 2011-08-21 03:56 1.7K phastCons12wayPrimate.txt.gz 2011-08-21 03:57 80M multiz12waySummary.sql 2011-08-21 03:57 1.5K multiz12waySummary.txt.gz 2011-08-21 03:57 23M multiz12wayFrames.sql 2011-08-21 03:57 1.7K multiz12wayFrames.txt.gz 2011-08-21 03:57 17M phastConsElements12wayPrimate.sql 2011-08-21 03:57 1.5K multiz12way.sql 2011-08-21 03:57 1.5K phastConsElements12wayPrimate.txt.gz 2011-08-21 03:57 3.2M multiz12way.txt.gz 2011-08-21 03:58 209M extFile.sql 2011-08-21 03:59 1.4K extFile.txt.gz 2011-08-21 03:59 81 phastCons12way.sql 2011-08-21 03:59 1.7K phastCons12way.txt.gz 2011-08-21 03:59 77M phyloP12way.sql 2011-08-21 03:59 1.7K phyloP12way.txt.gz 2011-08-21 04:00 86M chainMonDom5Link.sql 2011-11-14 03:05 1.5K chainMonDom5Link.txt.gz 2011-11-14 03:09 1.2G netMonDom5.sql 2011-11-14 03:18 2.0K netMonDom5.txt.gz 2011-11-14 03:18 31M chainMonDom5.sql 2011-11-14 03:18 1.6K chainMonDom5.txt.gz 2011-11-14 03:19 341M netGorGor3.sql 2011-11-27 14:04 2.0K netGorGor3.txt.gz 2011-11-27 14:04 16M chainGorGor3Link.sql 2011-11-27 14:04 1.5K chainGorGor3Link.txt.gz 2011-11-27 14:04 108M chainGorGor3.sql 2011-11-27 14:05 1.6K chainGorGor3.txt.gz 2011-11-27 14:05 28M tRNAs.sql 2012-04-23 09:16 1.7K tRNAs.txt.gz 2012-04-23 09:16 12K grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 234 cpgIslandExtUnmasked.sql 2014-06-01 18:26 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 18:26 1.0M augustusGene.sql 2015-07-26 17:21 1.9K augustusGene.txt.gz 2015-07-26 17:21 2.2M microsat.sql 2015-08-23 23:47 1.5K microsat.txt.gz 2015-08-23 23:47 349K all_est.sql 2016-07-17 10:50 2.1K all_est.txt.gz 2016-07-17 10:50 875K estOrientInfo.sql 2016-07-17 10:52 1.8K estOrientInfo.txt.gz 2016-07-17 10:52 221K intronEst.sql 2016-07-17 10:52 2.1K intronEst.txt.gz 2016-07-17 10:52 677K chromAlias.sql 2016-09-15 18:01 1.4K chromAlias.txt.gz 2016-09-15 18:01 134K all_mrna.sql 2020-05-08 18:29 2.1K all_mrna.txt.gz 2020-05-08 18:29 302K xenoMrna.sql 2020-08-22 18:48 2.1K xenoMrna.txt.gz 2020-08-22 18:48 321M refFlat.sql 2020-08-22 18:57 1.7K refGene.sql 2020-08-22 18:57 1.9K xenoRefGene.sql 2020-08-22 18:57 1.9K refGene.txt.gz 2020-08-22 18:57 217K refFlat.txt.gz 2020-08-22 18:57 200K xenoRefGene.txt.gz 2020-08-22 18:57 33M xenoRefFlat.sql 2020-08-22 19:12 1.7K xenoRefFlat.txt.gz 2020-08-22 19:12 30M mrnaOrientInfo.sql 2020-08-22 19:12 1.8K mrnaOrientInfo.txt.gz 2020-08-22 19:12 109K refSeqAli.sql 2020-08-22 19:12 2.1K refSeqAli.txt.gz 2020-08-22 19:12 224K xenoRefSeqAli.sql 2020-08-22 19:12 2.1K xenoRefSeqAli.txt.gz 2020-08-22 19:12 31M gbLoaded.sql 2020-08-22 19:12 1.6K gbLoaded.txt.gz 2020-08-22 19:12 41K tableDescriptions.sql 2020-10-10 02:03 1.4K tableDescriptions.txt.gz 2020-10-10 02:03 7.0K trackDb.sql 2021-06-10 16:54 2.1K trackDb.txt.gz 2021-06-10 16:54 45K hgFindSpec.sql 2021-06-10 16:54 1.8K hgFindSpec.txt.gz 2021-06-10 16:54 590 tableList.sql 2021-06-13 03:15 1.6K tableList.txt.gz 2021-06-13 03:15 4.5K bigFiles.sql 2021-06-13 03:15 1.4K bigFiles.txt.gz 2021-06-13 03:15 68