This directory contains a dump of the UCSC genome annotation database for the
    May 2019 (UMICH_Zoey_3.1/canFam5) assembly of the dog genome
    (canFam5, University of Michigan) .

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/85
    https://www.ncbi.nlm.nih.gov/genome/assembly/3218611
    https://www.ncbi.nlm.nih.gov/bioproject/318403
    https://www.ncbi.nlm.nih.gov/biosample/SAMN04851098

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=canFam5
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/canFam5/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/canFam5/database/ .
For a single file, e.g. gc5Base.txt.gz
    rsync -avzP 
        rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/gc5Base.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam5/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam5/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 canFam5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql canFam5 --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 2020-08-18 06:37 22M xenoRefSeqAli.sql 2020-08-18 06:37 2.1K xenoRefGene.txt.gz 2020-08-18 06:37 12M xenoRefGene.sql 2020-08-18 06:37 2.0K xenoRefFlat.txt.gz 2020-08-18 06:37 10M xenoRefFlat.sql 2020-08-18 06:37 1.7K xenoMrna.txt.gz 2020-08-18 06:09 221M xenoMrna.sql 2020-08-18 06:09 2.1K windowmaskerSdust.txt.gz 2020-07-28 08:54 124M windowmaskerSdust.sql 2020-07-28 08:54 1.5K ucscToINSDC.txt.gz 2020-07-29 14:00 6.7K ucscToINSDC.sql 2020-07-29 14:00 1.4K trackDb.txt.gz 2021-03-26 09:06 25K trackDb.sql 2021-03-26 09:06 2.1K tableList.txt.gz 2021-04-18 03:03 3.0K tableList.sql 2021-04-18 03:03 1.6K tableDescriptions.txt.gz 2021-01-13 06:05 5.8K tableDescriptions.sql 2021-01-13 06:05 1.4K simpleRepeat.txt.gz 2020-07-17 17:05 22M simpleRepeat.sql 2020-07-17 17:05 1.9K rmsk.txt.gz 2020-07-18 06:31 122M rmsk.sql 2020-07-18 06:31 1.9K refSeqAli.txt.gz 2020-08-18 06:37 191K refSeqAli.sql 2020-08-18 06:37 2.1K refGene.txt.gz 2020-08-18 06:37 181K refGene.sql 2020-08-18 06:37 1.9K refFlat.txt.gz 2020-08-18 06:37 168K refFlat.sql 2020-08-18 06:37 1.7K netMm39.txt.gz 2020-09-08 13:46 59M netMm39.sql 2020-09-08 13:46 2.1K netMm10.txt.gz 2020-08-17 13:09 59M netMm10.sql 2020-08-17 13:09 2.1K netHg38.txt.gz 2020-08-17 13:28 64M netHg38.sql 2020-08-17 13:28 2.1K nestedRepeats.txt.gz 2020-07-18 06:33 14M nestedRepeats.sql 2020-07-18 06:33 2.0K mrnaOrientInfo.txt.gz 2020-08-18 12:16 90K mrnaOrientInfo.sql 2020-08-18 12:16 1.8K microsat.txt.gz 2020-07-28 07:50 594K microsat.sql 2020-07-28 07:50 1.5K intronEst.txt.gz 2020-08-18 11:45 8.8M intronEst.sql 2020-08-18 11:45 2.1K history.txt.gz 2020-09-14 01:39 858 history.sql 2020-09-14 01:39 1.6K hgFindSpec.txt.gz 2021-03-26 09:06 804 hgFindSpec.sql 2021-03-26 09:06 1.8K grp.txt.gz 2020-07-17 16:00 213 grp.sql 2020-07-17 16:00 1.4K gold.txt.gz 2020-07-17 15:52 32K gold.sql 2020-07-17 15:52 1.7K genscan.txt.gz 2020-07-31 12:18 3.0M genscan.sql 2020-07-31 12:18 1.7K gc5BaseBw.txt.gz 2020-07-17 16:00 66 gc5BaseBw.sql 2020-07-17 16:00 1.3K gbLoaded.txt.gz 2020-08-18 12:19 1.4K gbLoaded.sql 2020-08-18 12:19 1.6K gap.txt.gz 2020-07-17 15:52 16K gap.sql 2020-07-17 15:52 1.6K estOrientInfo.txt.gz 2020-08-18 11:45 4.1M estOrientInfo.sql 2020-08-18 11:45 1.8K ensemblToGeneName.txt.gz 2020-09-01 09:31 208K ensemblToGeneName.sql 2020-09-01 09:31 1.4K ensemblSource.txt.gz 2020-09-01 11:12 135K ensemblSource.sql 2020-09-01 11:12 1.4K ensPep.txt.gz 2020-09-01 11:12 12M ensPep.sql 2020-09-01 11:12 1.3K ensGtp.txt.gz 2020-09-01 09:31 421K ensGtp.sql 2020-09-01 09:31 1.4K ensGene.txt.gz 2020-09-01 09:31 2.9M ensGene.sql 2020-09-01 09:31 1.9K cytoBandIdeo.txt.gz 2020-07-17 20:10 4.7K cytoBandIdeo.sql 2020-07-17 20:10 1.5K crisprAllTargets.txt.gz 2020-09-14 01:39 69 crisprAllTargets.sql 2020-09-14 01:39 1.3K cpgIslandExtUnmasked.txt.gz 2020-07-17 16:59 1.1M cpgIslandExtUnmasked.sql 2020-07-17 16:59 1.7K cpgIslandExt.txt.gz 2020-07-28 09:15 1.0M cpgIslandExt.sql 2020-07-28 09:15 1.7K chromInfo.txt.gz 2020-07-17 16:00 4.9K chromInfo.sql 2020-07-17 16:00 1.4K chromAlias.txt.gz 2020-07-29 13:24 8.4K chromAlias.sql 2020-07-29 13:24 1.4K chainMm39Link.txt.gz 2020-09-08 13:43 447M chainMm39Link.sql 2020-09-08 13:43 1.6K chainMm39.txt.gz 2020-09-08 13:40 53M chainMm39.sql 2020-09-08 13:40 1.7K chainMm10Link.txt.gz 2020-08-17 13:06 457M chainMm10Link.sql 2020-08-17 13:06 1.6K chainMm10.txt.gz 2020-08-17 13:03 55M chainMm10.sql 2020-08-17 13:03 1.7K chainHg38Link.txt.gz 2020-08-17 13:25 903M chainHg38Link.sql 2020-08-17 13:25 1.6K chainHg38.txt.gz 2020-08-17 13:19 204M chainHg38.sql 2020-08-17 13:19 1.7K bigFiles.txt.gz 2021-04-18 03:03 95 bigFiles.sql 2021-04-18 03:03 1.4K augustusGene.txt.gz 2020-07-29 16:48 2.3M augustusGene.sql 2020-07-29 16:48 2.0K all_mrna.txt.gz 2020-08-18 06:08 232K all_mrna.sql 2020-08-18 06:08 2.1K all_est.txt.gz 2020-08-18 11:45 16M all_est.sql 2020-08-18 11:45 2.1K