This directory contains a dump of the UCSC genome annotation database for the
    Jan. 2018 (Clint_PTRv2/panTro6) assembly of the chimp genome
    (panTro6, University of Washington) 
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:
    https://www.ncbi.nlm.nih.gov/genome/202
    https://www.ncbi.nlm.nih.gov/genome/assembly/1642151
    https://www.ncbi.nlm.nih.gov/bioproject/369439

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=panTro6
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.soe.ucsc.edu, then go to
the directory goldenPath/panTro6/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.soe.ucsc.edu/goldenPath/panTro6/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro6/database/gc5Base.txt.gz' 
        -O gc5Base.txt.gz

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 panTro6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro6 --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 - xenoRefSeqAli.txt.gz 2018-10-04 12:52 19M xenoRefSeqAli.sql 2018-10-04 12:52 2.1K xenoRefGene.txt.gz 2018-10-04 12:52 22M xenoRefGene.sql 2018-10-04 12:52 1.9K xenoRefFlat.txt.gz 2018-10-04 12:52 20M xenoRefFlat.sql 2018-10-04 12:52 1.7K xenoMrna.txt.gz 2018-10-04 12:51 231M xenoMrna.sql 2018-10-04 12:51 2.1K windowmaskerSdust.txt.gz 2018-10-04 12:50 147M windowmaskerSdust.sql 2018-10-04 12:50 1.5K ucscToRefSeq.txt.gz 2018-10-04 12:50 37K ucscToRefSeq.sql 2018-10-04 12:50 1.4K ucscToINSDC.txt.gz 2018-10-04 12:50 36K ucscToINSDC.sql 2018-10-04 12:50 1.4K trackDb.txt.gz 2021-06-10 16:55 45K trackDb.sql 2021-06-10 16:55 2.1K tableList.txt.gz 2021-06-13 03:04 3.4K tableList.sql 2021-06-13 03:04 1.6K tableDescriptions.txt.gz 2021-03-13 06:37 6.1K tableDescriptions.sql 2021-03-13 06:37 1.4K simpleRepeat.txt.gz 2018-10-04 12:50 27M simpleRepeat.sql 2018-10-04 12:50 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.5M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K rmsk.txt.gz 2018-10-04 12:49 140M rmsk.sql 2018-10-04 12:49 1.9K refSeqAli.txt.gz 2018-10-04 12:49 216K refSeqAli.sql 2018-10-04 12:49 2.1K refGene.txt.gz 2018-10-04 12:49 218K refGene.sql 2018-10-04 12:49 1.9K refFlat.txt.gz 2018-10-04 12:46 201K refFlat.sql 2018-10-04 12:46 1.7K netNeoSch1.txt.gz 2020-07-10 07:05 76M netNeoSch1.sql 2020-07-10 07:05 2.1K netMm39.txt.gz 2020-11-24 11:20 73M netMm39.sql 2020-11-24 11:20 2.1K netMm10.txt.gz 2018-10-04 12:45 73M netMm10.sql 2018-10-04 12:44 2.1K netHg38.txt.gz 2018-10-04 12:44 6.4M netHg38.sql 2018-10-04 12:44 2.1K nestedRepeats.txt.gz 2018-10-04 12:44 18M nestedRepeats.sql 2018-10-04 12:44 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 6.8M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.4M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 14M ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.6M ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 207K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 578K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:28 4.5M ncbiRefSeq.sql 2020-05-10 03:28 1.9K mrnaOrientInfo.txt.gz 2018-10-04 12:50 111K mrnaOrientInfo.sql 2018-10-04 12:50 1.8K microsat.txt.gz 2018-10-04 12:50 316K microsat.sql 2018-10-04 12:50 1.5K intronEst.txt.gz 2018-10-04 12:45 689K intronEst.sql 2018-10-04 12:45 2.1K hgFindSpec.txt.gz 2021-06-10 16:55 1.0K hgFindSpec.sql 2021-06-10 16:55 1.8K grp.txt.gz 2018-10-04 12:49 213 grp.sql 2018-10-04 12:49 1.3K gold.txt.gz 2018-10-04 12:50 68K gold.sql 2018-10-04 12:50 1.7K genscan.txt.gz 2018-10-04 12:50 2.9M genscan.sql 2018-10-04 12:50 1.7K gc5BaseBw.txt.gz 2018-10-04 12:50 66 gc5BaseBw.sql 2018-10-04 12:50 1.3K gap.txt.gz 2018-10-04 12:49 12K gap.sql 2018-10-04 12:49 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 extNcbiRefSeq.sql 2020-05-10 03:28 1.4K estOrientInfo.txt.gz 2018-10-04 12:49 225K estOrientInfo.sql 2018-10-04 12:49 1.8K cytoBandIdeo.txt.gz 2018-10-04 12:49 25K cytoBandIdeo.sql 2018-10-04 12:49 1.5K cpgIslandExtUnmasked.txt.gz 2018-10-04 12:49 1.0M cpgIslandExtUnmasked.sql 2018-10-04 12:49 1.7K cpgIslandExt.txt.gz 2018-10-04 12:49 634K cpgIslandExt.sql 2018-10-04 12:49 1.7K chromInfo.txt.gz 2018-10-04 12:49 25K chromInfo.sql 2018-10-04 12:49 1.4K chromAlias.txt.gz 2018-10-04 12:49 42K chromAlias.sql 2018-10-04 12:49 1.4K chainNeoSch1Link.txt.gz 2020-07-10 07:01 882M chainNeoSch1Link.sql 2020-07-10 07:01 1.5K chainNeoSch1.txt.gz 2020-07-10 06:54 229M chainNeoSch1.sql 2020-07-10 06:54 1.7K chainMm39Link.txt.gz 2020-11-24 11:17 512M chainMm39Link.sql 2020-11-24 11:17 1.6K chainMm39.txt.gz 2020-11-24 11:13 64M chainMm39.sql 2020-11-24 11:13 1.7K chainMm10Link.txt.gz 2018-10-04 12:47 515M chainMm10Link.sql 2018-10-04 12:46 1.5K chainMm10.txt.gz 2018-10-04 12:46 63M chainMm10.sql 2018-10-04 12:46 1.7K chainHg38Link.txt.gz 2018-10-04 12:45 214M chainHg38Link.sql 2018-10-04 12:45 1.5K chainHg38.txt.gz 2018-10-04 12:45 67M chainHg38.sql 2018-10-04 12:45 1.7K bigFiles.txt.gz 2021-06-13 03:04 95 bigFiles.sql 2021-06-13 03:04 1.4K augustusGene.txt.gz 2018-10-04 12:44 2.3M augustusGene.sql 2018-10-04 12:44 1.9K all_mrna.txt.gz 2018-10-04 12:44 297K all_mrna.sql 2018-10-04 12:44 2.1K all_est.txt.gz 2018-10-04 12:44 869K all_est.sql 2018-10-04 12:44 2.1K