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