This directory contains a dump of the UCSC genome annotation database for the
    Jan. 2018 (EquCab3.0/equCab3) assembly of the horse genome
    (equCab3, University of Louisville) .

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/145
    https://www.ncbi.nlm.nih.gov/genome/assembly/1512011
    https://www.ncbi.nlm.nih.gov/bioproject/421018

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=equCab3
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/equCab3/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/equCab3/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/equCab3/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab3/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab3/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 equCab3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql equCab3 --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 2019-07-25 16:50 2.1K all_est.txt.gz 2019-07-25 16:50 1.6M all_mrna.sql 2019-07-25 16:51 2.1K all_mrna.txt.gz 2019-07-25 16:51 1.5M augustusGene.sql 2019-07-25 16:51 1.9K augustusGene.txt.gz 2019-07-25 16:51 2.4M bigFiles.sql 2022-06-26 03:03 1.4K bigFiles.txt.gz 2022-06-26 03:03 95 chainHg38.sql 2019-07-25 16:51 1.7K chainHg38.txt.gz 2019-07-25 16:51 175M chainHg38Link.sql 2019-07-25 16:52 1.5K chainHg38Link.txt.gz 2019-07-25 16:53 884M chainMm10.sql 2019-07-25 16:56 1.7K chainMm10.txt.gz 2019-07-25 16:56 78M chainMm10Link.sql 2019-07-25 16:57 1.5K chainMm10Link.txt.gz 2019-07-25 16:57 631M chainMm39.sql 2020-11-24 18:59 1.7K chainMm39.txt.gz 2020-11-24 18:59 127M chainMm39Link.sql 2020-11-24 19:05 1.6K chainMm39Link.txt.gz 2020-11-24 19:05 798M chromAlias.sql 2019-07-25 17:00 1.4K chromAlias.txt.gz 2019-07-25 17:00 49K chromInfo.sql 2019-07-25 17:01 1.4K chromInfo.txt.gz 2019-07-25 17:01 27K cpgIslandExt.sql 2019-07-25 17:01 1.7K cpgIslandExt.txt.gz 2019-07-25 17:01 813K cpgIslandExtUnmasked.sql 2019-07-25 17:01 1.7K cpgIslandExtUnmasked.txt.gz 2019-07-25 17:01 967K cytoBandIdeo.sql 2019-07-25 17:01 1.5K cytoBandIdeo.txt.gz 2019-07-25 17:01 26K ensGene.sql 2021-05-25 14:31 1.9K ensGene.txt.gz 2021-05-25 14:31 3.3M ensGtp.sql 2021-05-25 14:31 1.4K ensGtp.txt.gz 2021-05-25 14:31 595K ensPep.sql 2021-05-25 14:34 1.3K ensPep.txt.gz 2021-05-25 14:34 16M ensemblSource.sql 2021-05-25 14:34 1.4K ensemblSource.txt.gz 2021-05-25 14:34 188K ensemblToGeneName.sql 2021-05-25 14:31 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:31 259K estOrientInfo.sql 2019-07-25 17:01 1.8K estOrientInfo.txt.gz 2019-07-25 17:01 517K extNcbiRefSeq.sql 2020-05-10 03:27 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:27 91 gap.sql 2019-07-25 17:01 1.6K gap.txt.gz 2019-07-25 17:01 86K gbLoaded.sql 2019-07-25 17:01 1.6K gbLoaded.txt.gz 2019-07-25 17:01 10K gc5BaseBw.sql 2019-07-25 17:01 1.3K gc5BaseBw.txt.gz 2019-07-25 17:01 66 genscan.sql 2019-07-25 17:02 1.7K genscan.txt.gz 2019-07-25 17:02 3.2M gold.sql 2019-07-25 17:02 1.7K gold.txt.gz 2019-07-25 17:02 182K grp.sql 2019-07-25 17:01 1.3K grp.txt.gz 2019-07-25 17:01 213 hgFindSpec.sql 2022-05-06 12:33 1.8K hgFindSpec.txt.gz 2022-05-06 12:33 1.2K hgFindSpec_pushedout.sql 2022-04-26 10:29 1.8K hgFindSpec_pushedout.txt.gz 2022-04-26 10:29 1.2K history.sql 2019-07-25 17:02 1.6K history.txt.gz 2019-07-25 17:02 736 intronEst.sql 2019-07-25 17:02 2.1K intronEst.txt.gz 2019-07-25 17:02 962K microsat.sql 2019-07-25 17:01 1.5K microsat.txt.gz 2019-07-25 17:01 119K mrnaOrientInfo.sql 2019-07-25 16:51 1.8K mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K ncbiRefSeq.sql 2020-05-10 03:27 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 418K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 127K ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 12M ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.7M ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.3M nestedRepeats.sql 2019-07-25 16:56 1.9K nestedRepeats.txt.gz 2019-07-25 16:56 12M netHg38.sql 2019-07-25 17:00 2.1K netHg38.txt.gz 2019-07-25 17:00 53M netMm10.sql 2019-07-25 17:00 2.1K netMm10.txt.gz 2019-07-25 17:01 68M netMm39.sql 2020-11-24 19:09 2.1K netMm39.txt.gz 2020-11-24 19:09 68M refFlat.sql 2019-07-25 17:01 1.7K refFlat.txt.gz 2019-07-25 17:01 122K refGene.sql 2019-07-25 17:01 1.9K refGene.txt.gz 2019-07-25 17:01 133K refSeqAli.sql 2019-07-25 16:50 2.1K refSeqAli.txt.gz 2019-07-25 16:50 132K rmsk.sql 2019-07-25 16:50 1.9K rmsk.txt.gz 2019-07-25 16:51 107M seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M simpleRepeat.sql 2019-07-25 16:51 1.9K simpleRepeat.txt.gz 2019-07-25 16:51 11M tableDescriptions.sql 2021-03-13 06:37 1.4K tableDescriptions.txt.gz 2021-03-13 06:37 6.4K tableList.sql 2022-06-26 03:03 1.6K tableList.txt.gz 2022-06-26 03:03 3.6K trackDb.sql 2022-05-06 12:33 2.1K trackDb.txt.gz 2022-05-06 12:33 49K trackDb_pushedout.sql 2022-04-26 10:29 2.1K trackDb_pushedout.txt.gz 2022-04-26 10:29 49K ucscToINSDC.sql 2019-07-25 17:01 1.4K ucscToINSDC.txt.gz 2019-07-25 17:01 41K ucscToRefSeq.sql 2019-07-25 17:01 1.4K ucscToRefSeq.txt.gz 2019-07-25 17:01 40K windowmaskerSdust.sql 2019-07-25 17:01 1.5K windowmaskerSdust.txt.gz 2019-07-25 17:01 138M xenoRefFlat.sql 2019-07-25 17:01 1.7K xenoRefFlat.txt.gz 2019-07-25 17:02 28M xenoRefGene.sql 2019-07-25 17:02 1.9K xenoRefGene.txt.gz 2019-07-25 17:02 31M xenoRefSeqAli.sql 2019-07-25 17:02 2.1K xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M