This directory contains a dump of the UCSC genome annotation database for the
    Oct. 2014 (Bison_UMD1.0/bisBis1) assembly of the bison genome
    (bisBis1, U. Maryland) .

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/8907
    http://www.ncbi.nlm.nih.gov/genome/assembly/237421
    http://www.ncbi.nlm.nih.gov/bioproject/266339 

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=bisBis1
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/bisBis1/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/bisBis1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/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 bisBis1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bisBis1 --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 - chainHg38Link.txt.gz 2017-04-07 12:10 1.0G chainMm10Link.txt.gz 2017-04-07 13:15 477M chainHg38.txt.gz 2017-04-07 11:48 315M rmsk.txt.gz 2017-04-07 13:50 148M windowmaskerSdust.txt.gz 2017-04-07 13:57 128M chainMm10.txt.gz 2017-04-07 13:07 70M netHg38.txt.gz 2017-04-07 13:41 68M netMm10.txt.gz 2017-04-07 13:45 55M xenoRefGene.txt.gz 2017-04-07 14:03 33M xenoRefSeqAli.txt.gz 2017-04-07 14:04 30M xenoRefFlat.txt.gz 2017-04-07 14:02 30M nestedRepeats.txt.gz 2017-04-07 13:37 14M simpleRepeat.txt.gz 2017-04-07 13:55 13M description.txt.gz 2017-04-07 13:39 13M gbSeq.txt.gz 2017-04-07 13:46 13M refLink.txt.gz 2017-04-07 13:47 11M gold.txt.gz 2017-04-07 13:38 9.5M gbCdnaInfo.txt.gz 2017-04-07 13:43 9.4M ensPep.txt.gz 2021-05-25 14:21 6.3M refSeqSummary.txt.gz 2017-04-07 13:48 5.2M author.txt.gz 2017-04-07 11:44 4.2M gbStatus.txt.gz 2017-04-07 13:47 3.9M gap.txt.gz 2017-04-07 13:43 3.9M productName.txt.gz 2017-04-07 13:47 3.6M genscan.txt.gz 2017-04-07 13:38 3.1M chromAlias.txt.gz 2020-04-12 03:25 3.0M ucscToINSDC.txt.gz 2017-04-07 13:56 2.9M geneName.txt.gz 2017-04-07 13:37 2.8M augustusGene.txt.gz 2017-04-07 11:44 2.2M ensGene.txt.gz 2021-05-25 14:19 2.2M cds.txt.gz 2017-04-07 11:44 2.1M cytoBandIdeo.txt.gz 2017-04-07 13:39 1.9M chromInfo.txt.gz 2017-04-07 13:38 1.8M cpgIslandExtUnmasked.txt.gz 2017-04-07 13:38 1.6M refSeqStatus.txt.gz 2017-04-07 13:47 1.5M ucscToRefSeq.txt.gz 2017-04-07 13:56 900K cpgIslandExt.txt.gz 2017-04-07 13:38 887K ensGtp.txt.gz 2021-05-25 14:19 341K source.txt.gz 2017-04-07 13:56 312K organism.txt.gz 2017-04-07 13:46 307K microsat.txt.gz 2017-04-07 11:45 193K ensemblToGeneName.txt.gz 2021-05-25 14:19 142K ensemblSource.txt.gz 2021-05-25 14:21 96K trackDb.txt.gz 2021-12-27 12:23 34K gbExtFile.txt.gz 2017-04-07 13:46 11K tableDescriptions.txt.gz 2020-04-12 03:25 7.2K tableList.txt.gz 2022-10-02 03:03 3.4K gbCdnaInfo.sql 2017-04-07 13:43 2.6K gbLoaded.txt.gz 2017-04-07 11:44 2.3K xenoRefSeqAli.sql 2017-04-07 14:04 2.1K refSeqAli.sql 2017-04-07 13:47 2.1K netMm10.sql 2017-04-07 13:43 2.1K netHg38.sql 2017-04-07 13:39 2.1K trackDb.sql 2021-12-27 12:23 2.1K ensGene.sql 2021-05-25 14:19 1.9K augustusGene.sql 2017-04-07 11:44 1.9K xenoRefGene.sql 2017-04-07 14:03 1.9K nestedRepeats.sql 2017-04-07 13:37 1.9K simpleRepeat.sql 2017-04-07 13:55 1.9K refGene.sql 2017-04-07 13:47 1.9K gbStatus.sql 2017-04-07 13:47 1.9K rmsk.sql 2017-04-07 13:48 1.9K mrnaOrientInfo.sql 2017-04-07 13:06 1.8K hgFindSpec.sql 2021-12-27 12:23 1.8K refLink.sql 2017-04-07 13:47 1.7K xenoRefFlat.sql 2017-04-07 14:02 1.7K cpgIslandExtUnmasked.sql 2017-04-07 13:38 1.7K refFlat.sql 2017-04-07 13:38 1.7K gbSeq.sql 2017-04-07 13:46 1.7K chainMm10.sql 2017-04-07 13:06 1.7K chainHg38.sql 2017-04-07 11:45 1.7K cpgIslandExt.sql 2017-04-07 13:38 1.7K genscan.sql 2017-04-07 13:38 1.7K gold.sql 2017-04-07 13:38 1.7K refSeqStatus.sql 2017-04-07 13:47 1.6K gap.sql 2017-04-07 13:43 1.6K gbLoaded.sql 2017-04-07 11:44 1.6K history.sql 2017-04-07 13:43 1.6K tableList.sql 2022-10-02 03:03 1.6K chainMm10Link.sql 2017-04-07 13:09 1.5K chainHg38Link.sql 2017-04-07 11:57 1.5K cytoBandIdeo.sql 2017-04-07 13:38 1.5K windowmaskerSdust.sql 2017-04-07 13:56 1.5K imageClone.sql 2017-04-07 13:46 1.5K refSeqSummary.sql 2017-04-07 13:48 1.5K microsat.sql 2017-04-07 11:45 1.5K gbMiscDiff.txt.gz 2017-04-07 13:46 1.5K gbMiscDiff.sql 2017-04-07 13:46 1.5K ensGtp.sql 2021-05-25 14:19 1.4K mrnaClone.txt.gz 2017-04-07 11:45 1.4K ucscToRefSeq.sql 2017-04-07 13:56 1.4K ucscToINSDC.sql 2017-04-07 13:56 1.4K chromAlias.sql 2020-04-12 03:25 1.4K productName.sql 2017-04-07 13:47 1.4K development.sql 2017-04-07 13:39 1.4K description.sql 2017-04-07 13:39 1.4K tableDescriptions.sql 2020-04-12 03:25 1.4K mrnaClone.sql 2017-04-07 11:45 1.4K ensemblToGeneName.sql 2021-05-25 14:19 1.4K organism.sql 2017-04-07 13:46 1.4K geneName.sql 2017-04-07 13:37 1.4K library.sql 2017-04-07 11:44 1.4K keyword.sql 2017-04-07 11:44 1.4K gbExtFile.sql 2017-04-07 13:46 1.4K tissue.sql 2017-04-07 13:56 1.4K source.sql 2017-04-07 13:56 1.4K author.sql 2017-04-07 11:44 1.4K cell.sql 2017-04-07 11:45 1.4K sex.sql 2017-04-07 13:55 1.4K cds.sql 2017-04-07 11:44 1.4K chromInfo.sql 2017-04-07 13:38 1.4K ensemblSource.sql 2021-05-25 14:21 1.4K bigFiles.sql 2022-10-02 03:03 1.4K grp.sql 2017-04-07 13:39 1.3K ensPep.sql 2021-05-25 14:21 1.3K gbWarn.sql 2017-04-07 11:57 1.3K gc5BaseBw.sql 2017-04-07 13:09 1.3K hgFindSpec.txt.gz 2021-12-27 12:23 769 keyword.txt.gz 2017-04-07 11:44 750 history.txt.gz 2017-04-07 13:43 573 tissue.txt.gz 2017-04-07 13:56 243 grp.txt.gz 2017-04-07 13:39 213 refGene.txt.gz 2017-04-07 13:47 106 refSeqAli.txt.gz 2017-04-07 13:47 103 refFlat.txt.gz 2017-04-07 13:38 93 mrnaOrientInfo.txt.gz 2017-04-07 13:06 84 bigFiles.txt.gz 2022-10-02 03:03 69 gc5BaseBw.txt.gz 2017-04-07 13:09 66 development.txt.gz 2017-04-07 13:39 63 library.txt.gz 2017-04-07 11:44 43 cell.txt.gz 2017-04-07 11:45 40 sex.txt.gz 2017-04-07 13:55 39 imageClone.txt.gz 2017-04-07 13:46 35 gbWarn.txt.gz 2017-04-07 11:57 31