This directory contains a dump of the UCSC genome annotation database for the
    May 2016 (Pan_tro 3.0/panTro5) assembly of the chimp genome
    (panTro5, Chimpanzee Sequencing and Analysis Consortium) 
from the Chimp Genome Sequencing Consortium.

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/202
    http://www.ncbi.nlm.nih.gov/genome/assembly/733711
    http://www.ncbi.nlm.nih.gov/bioproject/10627

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=panTro5
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/panTro5/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/panTro5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro5/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 panTro5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro5 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

-----------------------------------------------------------------------------
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_est.sql 2016-10-14 15:36 2.1K all_est.txt.gz 2016-10-14 15:36 889K all_mrna.sql 2020-08-22 17:50 2.1K all_mrna.txt.gz 2020-08-22 17:50 309K augustusGene.sql 2016-10-14 15:36 1.9K augustusGene.txt.gz 2016-10-14 15:36 2.4M bigFiles.sql 2022-06-26 03:04 1.4K bigFiles.txt.gz 2022-06-26 03:04 95 chainGorGor5.sql 2016-10-14 15:36 1.7K chainGorGor5.txt.gz 2016-10-14 15:37 83M chainGorGor5Link.sql 2016-10-14 15:37 1.5K chainGorGor5Link.txt.gz 2016-10-14 15:37 253M chainHg38.sql 2016-10-14 15:39 1.7K chainHg38.txt.gz 2016-10-14 15:39 61M chainHg38Link.sql 2016-10-14 15:40 1.5K chainHg38Link.txt.gz 2016-10-14 15:40 222M chainMm10.sql 2016-10-14 15:41 1.7K chainMm10.txt.gz 2016-10-14 15:41 67M chainMm10Link.sql 2016-10-14 15:41 1.5K chainMm10Link.txt.gz 2016-10-14 15:42 542M chainRn6.sql 2017-03-27 22:02 1.7K chainRn6.txt.gz 2017-03-27 22:13 1.0G chainRn6Link.sql 2017-03-27 22:47 1.5K chainRn6Link.txt.gz 2017-03-27 23:19 3.0G chromAlias.sql 2018-02-04 08:54 1.4K chromAlias.txt.gz 2018-02-04 08:54 467K chromInfo.sql 2016-10-14 15:45 1.4K chromInfo.txt.gz 2016-10-14 15:45 218K cpgIslandExt.sql 2016-10-14 15:45 1.7K cpgIslandExt.txt.gz 2016-10-14 15:45 707K cpgIslandExtUnmasked.sql 2016-10-14 15:45 1.7K cpgIslandExtUnmasked.txt.gz 2016-10-14 15:45 1.1M cytoBandIdeo.sql 2016-10-14 15:45 1.5K cytoBandIdeo.txt.gz 2016-10-14 15:45 235K ensGene.sql 2021-05-25 14:43 1.9K ensGene.txt.gz 2021-05-25 14:43 3.5M ensGtp.sql 2021-05-25 14:43 1.4K ensGtp.txt.gz 2021-05-25 14:43 617K ensPep.sql 2021-05-25 14:44 1.3K ensPep.txt.gz 2021-05-25 14:44 15M ensemblSource.sql 2021-05-25 14:44 1.4K ensemblSource.txt.gz 2021-05-25 14:44 181K ensemblToGeneName.sql 2021-05-25 14:43 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:43 310K estOrientInfo.sql 2016-10-14 15:45 1.8K estOrientInfo.txt.gz 2016-10-14 15:45 231K extNcbiRefSeq.sql 2021-02-10 16:00 1.5K extNcbiRefSeq.txt.gz 2021-02-10 16:00 91 gap.sql 2016-10-14 15:45 1.6K gap.txt.gz 2016-10-14 15:45 364K gbLoaded.sql 2020-08-22 18:06 1.6K gbLoaded.txt.gz 2020-08-22 18:06 38K gbMiscDiff.sql 2016-10-14 15:45 1.5K gbMiscDiff.txt.gz 2016-10-14 15:45 1.2M gc5BaseBw.sql 2016-10-14 15:46 1.3K gc5BaseBw.txt.gz 2016-10-14 15:46 66 genscan.sql 2016-10-14 15:45 1.7K genscan.txt.gz 2016-10-14 15:45 3.1M gold.sql 2016-10-14 15:46 1.7K gold.txt.gz 2016-10-14 15:46 1.1M grp.sql 2016-10-14 15:46 1.3K grp.txt.gz 2016-10-14 15:46 213 hgFindSpec.sql 2021-12-27 12:23 1.8K hgFindSpec.txt.gz 2021-12-27 12:23 1.2K history.sql 2016-10-14 15:36 1.6K history.txt.gz 2016-10-14 15:36 614 intronEst.sql 2016-10-14 15:37 2.1K intronEst.txt.gz 2016-10-14 15:37 705K microsat.sql 2016-10-14 15:40 1.5K microsat.txt.gz 2016-10-14 15:40 347K mrnaOrientInfo.sql 2020-08-22 17:50 1.8K mrnaOrientInfo.txt.gz 2020-08-22 17:50 115K ncbiRefSeq.sql 2021-02-10 15:25 2.0K ncbiRefSeq.txt.gz 2021-02-10 15:25 4.5M ncbiRefSeqCds.sql 2021-02-10 16:00 1.4K ncbiRefSeqCds.txt.gz 2021-02-10 16:00 565K ncbiRefSeqCurated.sql 2021-02-10 15:25 2.0K ncbiRefSeqCurated.txt.gz 2021-02-10 15:25 202K ncbiRefSeqLink.sql 2021-02-10 15:25 2.0K ncbiRefSeqLink.txt.gz 2021-02-10 15:25 2.5M ncbiRefSeqOther.sql 2021-02-10 16:00 1.3K ncbiRefSeqOther.txt.gz 2021-02-10 16:00 75 ncbiRefSeqPepTable.sql 2021-02-10 16:00 1.4K ncbiRefSeqPepTable.txt.gz 2021-02-10 16:00 13M ncbiRefSeqPredicted.sql 2021-02-10 15:25 2.0K ncbiRefSeqPredicted.txt.gz 2021-02-10 15:25 4.4M ncbiRefSeqPsl.sql 2021-02-10 15:25 2.1K ncbiRefSeqPsl.txt.gz 2021-02-10 15:25 6.6M nestedRepeats.sql 2016-10-14 15:45 1.9K nestedRepeats.txt.gz 2016-10-14 15:45 19M netGorGor5.sql 2016-10-14 15:45 2.1K netGorGor5.txt.gz 2016-10-14 15:45 9.5M netHg38.sql 2016-10-14 15:45 2.1K netHg38.txt.gz 2016-10-14 15:45 8.1M netMm10.sql 2016-10-14 15:45 2.1K netMm10.txt.gz 2016-10-14 15:45 75M netRn6.sql 2017-03-28 00:55 2.1K netRn6.txt.gz 2017-03-28 00:57 82M refFlat.sql 2020-08-22 17:50 1.7K refFlat.txt.gz 2020-08-22 17:50 206K refGene.sql 2020-08-22 17:50 1.9K refGene.txt.gz 2020-08-22 17:50 225K refSeqAli.sql 2020-08-22 17:50 2.1K refSeqAli.txt.gz 2020-08-22 17:50 229K rmsk.sql 2016-10-14 15:38 1.9K rmsk.txt.gz 2016-10-14 15:39 151M seqNcbiRefSeq.sql 2021-02-10 16:00 1.6K seqNcbiRefSeq.txt.gz 2021-02-10 16:00 1.5M simpleRepeat.sql 2016-10-14 15:41 1.9K simpleRepeat.txt.gz 2016-10-14 15:41 31M tableDescriptions.sql 2021-02-26 06:33 1.4K tableDescriptions.txt.gz 2021-02-26 06:33 6.5K tableList.sql 2022-06-26 03:04 1.6K tableList.txt.gz 2022-06-26 03:04 3.7K trackDb.sql 2021-12-27 12:23 2.1K trackDb.txt.gz 2021-12-27 12:23 40K ucscToINSDC.sql 2016-10-14 15:45 1.4K ucscToINSDC.txt.gz 2016-10-14 15:45 362K ucscToRefSeq.sql 2016-10-14 15:46 1.4K ucscToRefSeq.txt.gz 2016-10-14 15:46 353K windowmaskerSdust.sql 2016-10-14 15:46 1.5K windowmaskerSdust.txt.gz 2016-10-14 15:46 161M xenoMrna.sql 2020-08-22 17:50 2.1K xenoMrna.txt.gz 2020-08-22 17:50 257M xenoRefFlat.sql 2020-08-22 17:50 1.7K xenoRefFlat.txt.gz 2020-08-22 17:50 24M xenoRefGene.sql 2020-08-22 17:50 1.9K xenoRefGene.txt.gz 2020-08-22 17:50 27M xenoRefSeqAli.sql 2020-08-22 18:06 2.1K xenoRefSeqAli.txt.gz 2020-08-22 18:06 25M