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.
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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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gold.sql 2020-07-17 15:52 1.7K
gold.txt.gz 2020-07-17 15:52 32K
gap.sql 2020-07-17 15:52 1.6K
gap.txt.gz 2020-07-17 15:52 16K
grp.sql 2020-07-17 16:00 1.4K
grp.txt.gz 2020-07-17 16:00 213
chromInfo.sql 2020-07-17 16:00 1.4K
chromInfo.txt.gz 2020-07-17 16:00 4.9K
gc5BaseBw.sql 2020-07-17 16:00 1.3K
gc5BaseBw.txt.gz 2020-07-17 16:00 66
cpgIslandExtUnmasked.sql 2020-07-17 16:59 1.7K
cpgIslandExtUnmasked.txt.gz 2020-07-17 16:59 1.1M
simpleRepeat.sql 2020-07-17 17:05 1.9K
simpleRepeat.txt.gz 2020-07-17 17:05 22M
cytoBandIdeo.sql 2020-07-17 20:10 1.5K
cytoBandIdeo.txt.gz 2020-07-17 20:10 4.7K
rmsk.sql 2020-07-18 06:31 1.9K
rmsk.txt.gz 2020-07-18 06:31 122M
nestedRepeats.sql 2020-07-18 06:33 2.0K
nestedRepeats.txt.gz 2020-07-18 06:33 14M
microsat.sql 2020-07-28 07:50 1.5K
microsat.txt.gz 2020-07-28 07:50 594K
windowmaskerSdust.sql 2020-07-28 08:54 1.5K
windowmaskerSdust.txt.gz 2020-07-28 08:54 124M
cpgIslandExt.sql 2020-07-28 09:15 1.7K
cpgIslandExt.txt.gz 2020-07-28 09:15 1.0M
chromAlias.sql 2020-07-29 13:24 1.4K
chromAlias.txt.gz 2020-07-29 13:24 8.4K
ucscToINSDC.sql 2020-07-29 14:00 1.4K
ucscToINSDC.txt.gz 2020-07-29 14:00 6.7K
augustusGene.sql 2020-07-29 16:48 2.0K
augustusGene.txt.gz 2020-07-29 16:48 2.3M
genscan.sql 2020-07-31 12:18 1.7K
genscan.txt.gz 2020-07-31 12:18 3.0M
chainMm10.sql 2020-08-17 13:03 1.7K
chainMm10.txt.gz 2020-08-17 13:03 55M
chainMm10Link.sql 2020-08-17 13:06 1.6K
chainMm10Link.txt.gz 2020-08-17 13:06 457M
netMm10.sql 2020-08-17 13:09 2.1K
netMm10.txt.gz 2020-08-17 13:09 59M
chainHg38.sql 2020-08-17 13:19 1.7K
chainHg38.txt.gz 2020-08-17 13:19 204M
chainHg38Link.sql 2020-08-17 13:25 1.6K
chainHg38Link.txt.gz 2020-08-17 13:25 903M
netHg38.sql 2020-08-17 13:28 2.1K
netHg38.txt.gz 2020-08-17 13:28 64M
all_mrna.sql 2020-08-18 06:08 2.1K
all_mrna.txt.gz 2020-08-18 06:08 232K
xenoMrna.sql 2020-08-18 06:09 2.1K
xenoMrna.txt.gz 2020-08-18 06:09 221M
refGene.sql 2020-08-18 06:37 1.9K
refGene.txt.gz 2020-08-18 06:37 181K
refFlat.sql 2020-08-18 06:37 1.7K
refFlat.txt.gz 2020-08-18 06:37 168K
xenoRefGene.sql 2020-08-18 06:37 2.0K
xenoRefGene.txt.gz 2020-08-18 06:37 12M
xenoRefFlat.sql 2020-08-18 06:37 1.7K
xenoRefFlat.txt.gz 2020-08-18 06:37 10M
refSeqAli.sql 2020-08-18 06:37 2.1K
refSeqAli.txt.gz 2020-08-18 06:37 191K
xenoRefSeqAli.sql 2020-08-18 06:37 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 06:37 22M
estOrientInfo.sql 2020-08-18 11:45 1.8K
estOrientInfo.txt.gz 2020-08-18 11:45 4.1M
intronEst.sql 2020-08-18 11:45 2.1K
intronEst.txt.gz 2020-08-18 11:45 8.8M
all_est.sql 2020-08-18 11:45 2.1K
all_est.txt.gz 2020-08-18 11:45 16M
mrnaOrientInfo.sql 2020-08-18 12:16 1.8K
mrnaOrientInfo.txt.gz 2020-08-18 12:16 90K
gbLoaded.sql 2020-08-18 12:19 1.6K
gbLoaded.txt.gz 2020-08-18 12:19 1.4K
chainMm39.sql 2020-09-08 13:40 1.7K
chainMm39.txt.gz 2020-09-08 13:40 53M
chainMm39Link.sql 2020-09-08 13:43 1.6K
chainMm39Link.txt.gz 2020-09-08 13:43 447M
netMm39.sql 2020-09-08 13:46 2.1K
netMm39.txt.gz 2020-09-08 13:46 59M
crisprAllTargets.sql 2020-09-14 01:39 1.3K
crisprAllTargets.txt.gz 2020-09-14 01:39 69
history.sql 2020-09-14 01:39 1.6K
history.txt.gz 2020-09-14 01:39 858
ensGene.sql 2021-05-25 14:22 1.9K
ensGene.txt.gz 2021-05-25 14:22 2.9M
ensGtp.sql 2021-05-25 14:22 1.4K
ensGtp.txt.gz 2021-05-25 14:22 409K
ensemblToGeneName.sql 2021-05-25 14:22 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:22 94K
ensemblSource.sql 2021-05-25 14:23 1.4K
ensemblSource.txt.gz 2021-05-25 14:23 135K
ensPep.sql 2021-05-25 14:23 1.3K
ensPep.txt.gz 2021-05-25 14:23 12M
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 35K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 863
tableDescriptions.sql 2024-11-16 02:04 1.4K
tableDescriptions.txt.gz 2024-11-16 02:04 5.5K
tableList.sql 2024-11-17 03:13 1.6K
tableList.txt.gz 2024-11-17 03:13 3.0K
bigFiles.sql 2024-11-17 03:13 1.4K
bigFiles.txt.gz 2024-11-17 03:13 95