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 - xenoRefSeqAli.txt.gz 2019-07-25 17:02 30M xenoRefSeqAli.sql 2019-07-25 17:02 2.1K xenoRefGene.txt.gz 2019-07-25 17:02 31M xenoRefGene.sql 2019-07-25 17:02 1.9K xenoRefFlat.txt.gz 2019-07-25 17:02 28M xenoRefFlat.sql 2019-07-25 17:01 1.7K windowmaskerSdust.txt.gz 2019-07-25 17:01 138M windowmaskerSdust.sql 2019-07-25 17:01 1.5K ucscToRefSeq.txt.gz 2019-07-25 17:01 40K ucscToRefSeq.sql 2019-07-25 17:01 1.4K ucscToINSDC.txt.gz 2019-07-25 17:01 41K ucscToINSDC.sql 2019-07-25 17:01 1.4K trackDb.txt.gz 2024-07-25 09:34 69K trackDb.sql 2024-07-25 09:34 2.1K tableList.txt.gz 2024-12-01 03:05 3.4K tableList.sql 2024-12-01 03:05 1.6K tableDescriptions.txt.gz 2024-11-30 02:04 6.3K tableDescriptions.sql 2024-11-30 02:04 1.4K simpleRepeat.txt.gz 2019-07-25 16:51 11M simpleRepeat.sql 2019-07-25 16:51 1.9K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K rmsk.txt.gz 2019-07-25 16:51 107M rmsk.sql 2019-07-25 16:50 1.9K refSeqAli.txt.gz 2019-07-25 16:50 132K refSeqAli.sql 2019-07-25 16:50 2.1K refGene.txt.gz 2019-07-25 17:01 133K refGene.sql 2019-07-25 17:01 1.9K refFlat.txt.gz 2019-07-25 17:01 122K refFlat.sql 2019-07-25 17:01 1.7K netMm39.txt.gz 2020-11-24 19:09 68M netMm39.sql 2020-11-24 19:09 2.1K netMm10.txt.gz 2019-07-25 17:01 68M netMm10.sql 2019-07-25 17:00 2.1K netHg38.txt.gz 2019-07-25 17:00 53M netHg38.sql 2019-07-25 17:00 2.1K nestedRepeats.txt.gz 2019-07-25 16:56 12M nestedRepeats.sql 2019-07-25 16:56 1.9K ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.3M ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.7M ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 12M ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 127K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 418K ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ncbiRefSeq.txt.gz 2020-05-10 03:27 3.8M ncbiRefSeq.sql 2020-05-10 03:27 1.9K mrnaOrientInfo.txt.gz 2019-07-25 16:51 470K mrnaOrientInfo.sql 2019-07-25 16:51 1.8K microsat.txt.gz 2019-07-25 17:01 119K microsat.sql 2019-07-25 17:01 1.5K intronEst.txt.gz 2019-07-25 17:02 962K intronEst.sql 2019-07-25 17:02 2.1K history.txt.gz 2019-07-25 17:02 736 history.sql 2019-07-25 17:02 1.6K hgFindSpec.txt.gz 2024-07-25 09:34 1.3K hgFindSpec.sql 2024-07-25 09:34 1.8K grp.txt.gz 2019-07-25 17:01 213 grp.sql 2019-07-25 17:01 1.3K gold.txt.gz 2019-07-25 17:02 182K gold.sql 2019-07-25 17:02 1.7K genscan.txt.gz 2019-07-25 17:02 3.2M genscan.sql 2019-07-25 17:02 1.7K gc5BaseBw.txt.gz 2019-07-25 17:01 66 gc5BaseBw.sql 2019-07-25 17:01 1.3K gbLoaded.txt.gz 2019-07-25 17:01 10K gbLoaded.sql 2019-07-25 17:01 1.6K gap.txt.gz 2019-07-25 17:01 86K gap.sql 2019-07-25 17:01 1.6K extNcbiRefSeq.txt.gz 2020-05-10 03:27 91 extNcbiRefSeq.sql 2020-05-10 03:27 1.4K estOrientInfo.txt.gz 2019-07-25 17:01 517K estOrientInfo.sql 2019-07-25 17:01 1.8K ensemblToGeneName.txt.gz 2021-05-25 14:31 259K ensemblToGeneName.sql 2021-05-25 14:31 1.4K ensemblSource.txt.gz 2021-05-25 14:34 188K ensemblSource.sql 2021-05-25 14:34 1.4K ensPep.txt.gz 2021-05-25 14:34 16M ensPep.sql 2021-05-25 14:34 1.3K ensGtp.txt.gz 2021-05-25 14:31 595K ensGtp.sql 2021-05-25 14:31 1.4K ensGene.txt.gz 2021-05-25 14:31 3.3M ensGene.sql 2021-05-25 14:31 1.9K cytoBandIdeo.txt.gz 2019-07-25 17:01 26K cytoBandIdeo.sql 2019-07-25 17:01 1.5K cpgIslandExtUnmasked.txt.gz 2019-07-25 17:01 967K cpgIslandExtUnmasked.sql 2019-07-25 17:01 1.7K cpgIslandExt.txt.gz 2019-07-25 17:01 813K cpgIslandExt.sql 2019-07-25 17:01 1.7K chromInfo.txt.gz 2019-07-25 17:01 27K chromInfo.sql 2019-07-25 17:01 1.4K chromAlias.txt.gz 2019-07-25 17:00 49K chromAlias.sql 2019-07-25 17:00 1.4K chainMm39Link.txt.gz 2020-11-24 19:05 798M chainMm39Link.sql 2020-11-24 19:05 1.6K chainMm39.txt.gz 2020-11-24 18:59 127M chainMm39.sql 2020-11-24 18:59 1.7K chainMm10Link.txt.gz 2019-07-25 16:57 631M chainMm10Link.sql 2019-07-25 16:57 1.5K chainMm10.txt.gz 2019-07-25 16:56 78M chainMm10.sql 2019-07-25 16:56 1.7K chainHg38Link.txt.gz 2019-07-25 16:53 884M chainHg38Link.sql 2019-07-25 16:52 1.5K chainHg38.txt.gz 2019-07-25 16:51 175M chainHg38.sql 2019-07-25 16:51 1.7K bigFiles.txt.gz 2024-12-01 03:05 95 bigFiles.sql 2024-12-01 03:05 1.4K augustusGene.txt.gz 2019-07-25 16:51 2.4M augustusGene.sql 2019-07-25 16:51 1.9K all_mrna.txt.gz 2019-07-25 16:51 1.5M all_mrna.sql 2019-07-25 16:51 2.1K all_est.txt.gz 2019-07-25 16:50 1.6M all_est.sql 2019-07-25 16:50 2.1K