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