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;'

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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 - gc5BaseBw.txt.gz 2019-07-25 17:01 66 ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 extNcbiRefSeq.txt.gz 2020-05-10 03:27 91 bigFiles.txt.gz 2024-04-21 03:06 95 grp.txt.gz 2019-07-25 17:01 213 history.txt.gz 2019-07-25 17:02 736 gc5BaseBw.sql 2019-07-25 17:01 1.3K hgFindSpec.txt.gz 2024-01-31 15:13 1.3K hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ensPep.sql 2021-05-25 14:34 1.3K grp.sql 2019-07-25 17:01 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ensemblSource.sql 2021-05-25 14:34 1.4K chromInfo.sql 2019-07-25 17:01 1.4K bigFiles.sql 2024-04-21 03:06 1.4K ensemblToGeneName.sql 2021-05-25 14:31 1.4K chromAlias.sql 2019-07-25 17:00 1.4K ucscToINSDC.sql 2019-07-25 17:01 1.4K ucscToRefSeq.sql 2019-07-25 17:01 1.4K extNcbiRefSeq.sql 2020-05-10 03:27 1.4K ensGtp.sql 2021-05-25 14:31 1.4K tableDescriptions.sql 2024-04-20 02:04 1.5K microsat.sql 2019-07-25 17:01 1.5K windowmaskerSdust.sql 2019-07-25 17:01 1.5K cytoBandIdeo.sql 2019-07-25 17:01 1.5K chainHg38Link.sql 2019-07-25 16:52 1.5K chainMm10Link.sql 2019-07-25 16:57 1.5K seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K chainMm39Link.sql 2020-11-24 19:05 1.6K history.sql 2019-07-25 17:02 1.6K gbLoaded.sql 2019-07-25 17:01 1.6K tableList.sql 2024-04-21 03:06 1.6K gap.sql 2019-07-25 17:01 1.6K gold.sql 2019-07-25 17:02 1.7K genscan.sql 2019-07-25 17:02 1.7K cpgIslandExt.sql 2019-07-25 17:01 1.7K chainHg38.sql 2019-07-25 16:51 1.7K chainMm10.sql 2019-07-25 16:56 1.7K refFlat.sql 2019-07-25 17:01 1.7K cpgIslandExtUnmasked.sql 2019-07-25 17:01 1.7K xenoRefFlat.sql 2019-07-25 17:01 1.7K chainMm39.sql 2020-11-24 18:59 1.7K hgFindSpec.sql 2024-01-31 15:13 1.8K estOrientInfo.sql 2019-07-25 17:01 1.8K mrnaOrientInfo.sql 2019-07-25 16:51 1.8K hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K rmsk.sql 2019-07-25 16:50 1.9K refGene.sql 2019-07-25 17:01 1.9K simpleRepeat.sql 2019-07-25 16:51 1.9K ncbiRefSeq.sql 2020-05-10 03:27 1.9K nestedRepeats.sql 2019-07-25 16:56 1.9K xenoRefGene.sql 2019-07-25 17:02 1.9K augustusGene.sql 2019-07-25 16:51 1.9K ensGene.sql 2021-05-25 14:31 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K trackDb.sql 2024-01-31 15:13 2.1K trackDb_pushedout.sql 2023-12-05 13:51 2.1K netHg38.sql 2019-07-25 17:00 2.1K netMm10.sql 2019-07-25 17:00 2.1K all_est.sql 2019-07-25 16:50 2.1K all_mrna.sql 2019-07-25 16:51 2.1K intronEst.sql 2019-07-25 17:02 2.1K refSeqAli.sql 2019-07-25 16:50 2.1K netMm39.sql 2020-11-24 19:09 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K xenoRefSeqAli.sql 2019-07-25 17:02 2.1K tableList.txt.gz 2024-04-21 03:06 3.6K tableDescriptions.txt.gz 2024-04-20 02:04 6.3K gbLoaded.txt.gz 2019-07-25 17:01 10K cytoBandIdeo.txt.gz 2019-07-25 17:01 26K chromInfo.txt.gz 2019-07-25 17:01 27K trackDb_pushedout.txt.gz 2023-12-05 13:51 32K ucscToRefSeq.txt.gz 2019-07-25 17:01 40K ucscToINSDC.txt.gz 2019-07-25 17:01 41K chromAlias.txt.gz 2019-07-25 17:00 49K trackDb.txt.gz 2024-01-31 15:13 54K gap.txt.gz 2019-07-25 17:01 86K microsat.txt.gz 2019-07-25 17:01 119K refFlat.txt.gz 2019-07-25 17:01 122K ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 127K refSeqAli.txt.gz 2019-07-25 16:50 132K refGene.txt.gz 2019-07-25 17:01 133K gold.txt.gz 2019-07-25 17:02 182K ensemblSource.txt.gz 2021-05-25 14:34 188K ensemblToGeneName.txt.gz 2021-05-25 14:31 259K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 418K mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K estOrientInfo.txt.gz 2019-07-25 17:01 517K ensGtp.txt.gz 2021-05-25 14:31 595K cpgIslandExt.txt.gz 2019-07-25 17:01 813K intronEst.txt.gz 2019-07-25 17:02 962K cpgIslandExtUnmasked.txt.gz 2019-07-25 17:01 967K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M all_mrna.txt.gz 2019-07-25 16:51 1.5M all_est.txt.gz 2019-07-25 16:50 1.6M ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M augustusGene.txt.gz 2019-07-25 16:51 2.4M genscan.txt.gz 2019-07-25 17:02 3.2M ensGene.txt.gz 2021-05-25 14:31 3.3M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.7M ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.3M simpleRepeat.txt.gz 2019-07-25 16:51 11M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 12M nestedRepeats.txt.gz 2019-07-25 16:56 12M ensPep.txt.gz 2021-05-25 14:34 16M xenoRefFlat.txt.gz 2019-07-25 17:02 28M xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M xenoRefGene.txt.gz 2019-07-25 17:02 31M netHg38.txt.gz 2019-07-25 17:00 53M netMm10.txt.gz 2019-07-25 17:01 68M netMm39.txt.gz 2020-11-24 19:09 68M chainMm10.txt.gz 2019-07-25 16:56 78M rmsk.txt.gz 2019-07-25 16:51 107M chainMm39.txt.gz 2020-11-24 18:59 127M windowmaskerSdust.txt.gz 2019-07-25 17:01 138M chainHg38.txt.gz 2019-07-25 16:51 175M chainMm10Link.txt.gz 2019-07-25 16:57 631M chainMm39Link.txt.gz 2020-11-24 19:05 798M chainHg38Link.txt.gz 2019-07-25 16:53 884M