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 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 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 mrnaOrientInfo.sql 2019-07-25 16:51 1.8K mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K simpleRepeat.sql 2019-07-25 16:51 1.9K simpleRepeat.txt.gz 2019-07-25 16:51 11M 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 nestedRepeats.sql 2019-07-25 16:56 1.9K nestedRepeats.txt.gz 2019-07-25 16:56 12M 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 netHg38.sql 2019-07-25 17:00 2.1K netHg38.txt.gz 2019-07-25 17:00 53M chromAlias.sql 2019-07-25 17:00 1.4K chromAlias.txt.gz 2019-07-25 17:00 49K netMm10.sql 2019-07-25 17:00 2.1K netMm10.txt.gz 2019-07-25 17:01 68M 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 grp.sql 2019-07-25 17:01 1.3K grp.txt.gz 2019-07-25 17:01 213 refFlat.sql 2019-07-25 17:01 1.7K refFlat.txt.gz 2019-07-25 17:01 122K cytoBandIdeo.sql 2019-07-25 17:01 1.5K cytoBandIdeo.txt.gz 2019-07-25 17:01 26K estOrientInfo.sql 2019-07-25 17:01 1.8K estOrientInfo.txt.gz 2019-07-25 17:01 517K 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 microsat.sql 2019-07-25 17:01 1.5K microsat.txt.gz 2019-07-25 17:01 119K refGene.sql 2019-07-25 17:01 1.9K refGene.txt.gz 2019-07-25 17:01 133K 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 gc5BaseBw.sql 2019-07-25 17:01 1.3K gc5BaseBw.txt.gz 2019-07-25 17:01 66 xenoRefFlat.sql 2019-07-25 17:01 1.7K xenoRefFlat.txt.gz 2019-07-25 17:02 28M genscan.sql 2019-07-25 17:02 1.7K genscan.txt.gz 2019-07-25 17:02 3.2M xenoRefGene.sql 2019-07-25 17:02 1.9K xenoRefGene.txt.gz 2019-07-25 17:02 31M gold.sql 2019-07-25 17:02 1.7K gold.txt.gz 2019-07-25 17:02 182K xenoRefSeqAli.sql 2019-07-25 17:02 2.1K xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M 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 ncbiRefSeq.sql 2020-05-10 03:27 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M extNcbiRefSeq.sql 2020-05-10 03:27 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:27 91 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 seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M 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 netMm39.sql 2020-11-24 19:09 2.1K netMm39.txt.gz 2020-11-24 19:09 68M 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 ensemblToGeneName.sql 2021-05-25 14:31 1.4K ensemblToGeneName.txt.gz 2021-05-25 14:31 259K ensemblSource.sql 2021-05-25 14:34 1.4K ensemblSource.txt.gz 2021-05-25 14:34 188K ensPep.sql 2021-05-25 14:34 1.3K ensPep.txt.gz 2021-05-25 14:34 16M trackDb_pushedout.sql 2023-12-05 13:51 2.1K trackDb_pushedout.txt.gz 2023-12-05 13:51 32K hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K trackDb.sql 2024-01-31 15:13 2.1K trackDb.txt.gz 2024-01-31 15:13 54K hgFindSpec.sql 2024-01-31 15:13 1.8K hgFindSpec.txt.gz 2024-01-31 15:13 1.3K tableDescriptions.sql 2024-04-20 02:04 1.5K tableDescriptions.txt.gz 2024-04-20 02:04 6.3K tableList.sql 2024-04-21 03:06 1.6K tableList.txt.gz 2024-04-21 03:06 3.6K bigFiles.sql 2024-04-21 03:06 1.4K bigFiles.txt.gz 2024-04-21 03:06 95