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