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;'

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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 - chainNeoSch1Link.txt.gz 2020-07-10 07:01 882M chainMm10Link.txt.gz 2018-10-04 12:47 515M chainMm39Link.txt.gz 2020-11-24 11:17 512M xenoMrna.txt.gz 2018-10-04 12:51 231M chainNeoSch1.txt.gz 2020-07-10 06:54 229M chainHg38Link.txt.gz 2018-10-04 12:45 214M windowmaskerSdust.txt.gz 2018-10-04 12:50 147M rmsk.txt.gz 2018-10-04 12:49 140M netNeoSch1.txt.gz 2020-07-10 07:05 76M netMm39.txt.gz 2020-11-24 11:20 73M netMm10.txt.gz 2018-10-04 12:45 73M chainHg38.txt.gz 2018-10-04 12:45 67M chainMm39.txt.gz 2020-11-24 11:13 64M chainMm10.txt.gz 2018-10-04 12:46 63M simpleRepeat.txt.gz 2018-10-04 12:50 27M xenoRefGene.txt.gz 2018-10-04 12:52 22M xenoRefFlat.txt.gz 2018-10-04 12:52 20M xenoRefSeqAli.txt.gz 2018-10-04 12:52 19M nestedRepeats.txt.gz 2018-10-04 12:44 18M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 14M ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 6.8M netHg38.txt.gz 2018-10-04 12:44 6.4M ncbiRefSeq.txt.gz 2020-05-10 03:28 4.5M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 4.4M genscan.txt.gz 2018-10-04 12:50 2.9M ncbiRefSeqLink.txt.gz 2020-05-10 03:28 2.6M augustusGene.txt.gz 2018-10-04 12:44 2.3M seqNcbiRefSeq.txt.gz 2020-05-10 03:28 1.5M cpgIslandExtUnmasked.txt.gz 2018-10-04 12:49 1.0M all_est.txt.gz 2018-10-04 12:44 869K intronEst.txt.gz 2018-10-04 12:45 689K cpgIslandExt.txt.gz 2018-10-04 12:49 634K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 578K microsat.txt.gz 2018-10-04 12:50 316K all_mrna.txt.gz 2018-10-04 12:44 297K estOrientInfo.txt.gz 2018-10-04 12:49 225K refGene.txt.gz 2018-10-04 12:49 218K refSeqAli.txt.gz 2018-10-04 12:49 216K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 207K refFlat.txt.gz 2018-10-04 12:46 201K mrnaOrientInfo.txt.gz 2018-10-04 12:50 111K gold.txt.gz 2018-10-04 12:50 68K trackDb.txt.gz 2024-01-31 15:13 51K chromAlias.txt.gz 2018-10-04 12:49 42K ucscToRefSeq.txt.gz 2018-10-04 12:50 37K ucscToINSDC.txt.gz 2018-10-04 12:50 36K trackDb_pushedout.txt.gz 2023-12-05 13:52 33K cytoBandIdeo.txt.gz 2018-10-04 12:49 25K chromInfo.txt.gz 2018-10-04 12:49 25K gap.txt.gz 2018-10-04 12:49 12K tableDescriptions.txt.gz 2024-03-23 02:03 6.1K tableList.txt.gz 2024-03-24 03:07 3.5K xenoRefSeqAli.sql 2018-10-04 12:52 2.1K netNeoSch1.sql 2020-07-10 07:05 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K netMm39.sql 2020-11-24 11:20 2.1K refSeqAli.sql 2018-10-04 12:49 2.1K intronEst.sql 2018-10-04 12:45 2.1K xenoMrna.sql 2018-10-04 12:51 2.1K all_mrna.sql 2018-10-04 12:44 2.1K all_est.sql 2018-10-04 12:44 2.1K netMm10.sql 2018-10-04 12:44 2.1K netHg38.sql 2018-10-04 12:44 2.1K trackDb_pushedout.sql 2023-12-05 13:52 2.1K trackDb.sql 2024-01-31 15:13 2.1K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K augustusGene.sql 2018-10-04 12:44 1.9K xenoRefGene.sql 2018-10-04 12:52 1.9K nestedRepeats.sql 2018-10-04 12:44 1.9K ncbiRefSeq.sql 2020-05-10 03:28 1.9K simpleRepeat.sql 2018-10-04 12:50 1.9K refGene.sql 2018-10-04 12:49 1.9K rmsk.sql 2018-10-04 12:49 1.9K hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K mrnaOrientInfo.sql 2018-10-04 12:50 1.8K estOrientInfo.sql 2018-10-04 12:49 1.8K hgFindSpec.sql 2024-01-31 15:13 1.8K chainNeoSch1.sql 2020-07-10 06:54 1.7K chainMm39.sql 2020-11-24 11:13 1.7K xenoRefFlat.sql 2018-10-04 12:52 1.7K cpgIslandExtUnmasked.sql 2018-10-04 12:49 1.7K refFlat.sql 2018-10-04 12:46 1.7K chainMm10.sql 2018-10-04 12:46 1.7K chainHg38.sql 2018-10-04 12:45 1.7K cpgIslandExt.sql 2018-10-04 12:49 1.7K genscan.sql 2018-10-04 12:50 1.7K gold.sql 2018-10-04 12:50 1.7K gap.sql 2018-10-04 12:49 1.6K chainNeoSch1Link.sql 2020-07-10 07:01 1.6K tableList.sql 2024-03-24 03:07 1.6K chainMm39Link.sql 2020-11-24 11:17 1.6K seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K chainMm10Link.sql 2018-10-04 12:46 1.5K chainHg38Link.sql 2018-10-04 12:45 1.5K cytoBandIdeo.sql 2018-10-04 12:49 1.5K windowmaskerSdust.sql 2018-10-04 12:50 1.5K microsat.sql 2018-10-04 12:50 1.5K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K ucscToRefSeq.sql 2018-10-04 12:50 1.4K tableDescriptions.sql 2024-03-23 02:03 1.4K ucscToINSDC.sql 2018-10-04 12:50 1.4K chromAlias.sql 2018-10-04 12:49 1.4K chromInfo.sql 2018-10-04 12:49 1.4K bigFiles.sql 2024-03-24 03:07 1.4K ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K grp.sql 2018-10-04 12:49 1.3K ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K gc5BaseBw.sql 2018-10-04 12:50 1.3K hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.1K hgFindSpec.txt.gz 2024-01-31 15:13 1.1K grp.txt.gz 2018-10-04 12:49 213 bigFiles.txt.gz 2024-03-24 03:07 95 extNcbiRefSeq.txt.gz 2020-05-10 03:28 91 ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 gc5BaseBw.txt.gz 2018-10-04 12:50 66