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 -
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 2021-05-25 14:23 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 2021-05-25 14:22 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 2021-05-25 14:22 409K
all_mrna.txt.gz 2020-08-18 06:08 232K
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 2021-05-25 14:23 135K
ensemblToGeneName.txt.gz 2021-05-25 14:22 94K
mrnaOrientInfo.txt.gz 2020-08-18 12:16 90K
trackDb.txt.gz 2024-01-31 15:13 35K
gold.txt.gz 2020-07-17 15:52 32K
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 2024-11-23 02:04 5.5K
chromInfo.txt.gz 2020-07-17 16:00 4.9K
cytoBandIdeo.txt.gz 2020-07-17 20:10 4.7K
tableList.txt.gz 2024-11-24 03:04 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 2024-01-31 15:13 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 2021-05-25 14:22 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 2024-01-31 15:13 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 2024-11-24 03:04 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 2021-05-25 14:22 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
chromInfo.sql 2020-07-17 16:00 1.4K
ensemblToGeneName.sql 2021-05-25 14:22 1.4K
bigFiles.sql 2024-11-24 03:04 1.4K
ensemblSource.sql 2021-05-25 14:23 1.4K
grp.sql 2020-07-17 16:00 1.4K
gbLoaded.txt.gz 2020-08-18 12:19 1.4K
ensPep.sql 2021-05-25 14:23 1.3K
crisprAllTargets.sql 2020-09-14 01:39 1.3K
gc5BaseBw.sql 2020-07-17 16:00 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 863
history.txt.gz 2020-09-14 01:39 858
grp.txt.gz 2020-07-17 16:00 213
bigFiles.txt.gz 2024-11-24 03:04 95
crisprAllTargets.txt.gz 2020-09-14 01:39 69
gc5BaseBw.txt.gz 2020-07-17 16:00 66