This directory contains a dump of the UCSC genome annotation database for the
Oct. 2020 (Dog10K_Boxer_Tasha/canFam6) assembly of the dog genome
(canFam6, Dog Genome Sequencing Consortium) .
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/8227741
https://www.ncbi.nlm.nih.gov/bioproject/13179
https://www.ncbi.nlm.nih.gov/biosample/SAMN02953603
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=canFam6
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/canFam6/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/canFam6/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam6/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 canFam6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql canFam6 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
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 2021-05-18 09:37 914M
chainMm10Link.txt.gz 2021-05-18 09:17 455M
chainMm39Link.txt.gz 2021-05-18 20:14 421M
xenoMrna.txt.gz 2021-05-18 10:08 218M
chainHg38.txt.gz 2021-05-18 09:29 211M
windowmaskerSdust.txt.gz 2021-05-12 18:25 123M
rmsk.txt.gz 2021-05-12 18:55 121M
netHg38.txt.gz 2021-05-18 09:40 63M
netMm39.txt.gz 2021-05-18 20:17 58M
netMm10.txt.gz 2021-05-18 09:20 58M
chainMm10.txt.gz 2021-05-18 09:13 55M
chainMm39.txt.gz 2021-05-18 20:11 48M
simpleRepeat.txt.gz 2021-05-12 15:31 22M
xenoRefSeqAli.txt.gz 2021-05-18 10:36 21M
all_est.txt.gz 2021-05-18 12:15 16M
nestedRepeats.txt.gz 2021-05-12 18:57 14M
ncbiRefSeqPepTable.txt.gz 2021-05-13 11:16 12M
xenoRefGene.txt.gz 2021-05-18 10:35 11M
xenoRefFlat.txt.gz 2021-05-18 10:36 10M
intronEst.txt.gz 2021-05-18 12:15 8.7M
ncbiRefSeqPsl.txt.gz 2021-05-13 11:14 6.1M
ncbiRefSeq.txt.gz 2021-05-13 11:14 4.3M
estOrientInfo.txt.gz 2021-05-18 12:15 4.1M
ncbiRefSeqPredicted.txt.gz 2021-05-13 11:14 4.1M
genscan.txt.gz 2021-05-13 11:26 2.9M
ncbiRefSeqLink.txt.gz 2021-05-13 11:14 2.4M
augustusGene.txt.gz 2021-05-13 13:41 2.2M
seqNcbiRefSeq.txt.gz 2021-05-13 11:16 1.4M
cpgIslandExtUnmasked.txt.gz 2021-05-12 15:00 1.1M
cpgIslandExt.txt.gz 2021-05-13 10:40 1.0M
microsat.txt.gz 2021-05-12 16:58 576K
ncbiRefSeqCds.txt.gz 2021-05-13 11:16 433K
all_mrna.txt.gz 2021-05-18 10:07 221K
refSeqAli.txt.gz 2021-05-18 10:36 185K
ncbiRefSeqCurated.txt.gz 2021-05-13 11:14 184K
refGene.txt.gz 2021-05-18 10:35 178K
refFlat.txt.gz 2021-05-18 10:35 165K
mrnaOrientInfo.txt.gz 2021-05-18 12:15 87K
trackDb.txt.gz 2023-12-05 13:53 31K
gold.txt.gz 2021-05-12 11:40 22K
gap.txt.gz 2021-05-12 11:40 13K
tableDescriptions.txt.gz 2024-11-23 02:04 6.0K
tableList.txt.gz 2024-11-24 03:04 3.2K
chromAlias.txt.gz 2021-05-13 10:21 2.2K
xenoRefSeqAli.sql 2021-05-18 10:36 2.1K
ncbiRefSeqPsl.sql 2021-05-13 11:14 2.1K
refSeqAli.sql 2021-05-18 10:36 2.1K
intronEst.sql 2021-05-18 12:15 2.1K
xenoMrna.sql 2021-05-18 10:08 2.1K
all_mrna.sql 2021-05-18 10:07 2.1K
all_est.sql 2021-05-18 12:15 2.1K
netMm39.sql 2021-05-18 20:17 2.1K
netMm10.sql 2021-05-18 09:20 2.1K
netHg38.sql 2021-05-18 09:40 2.1K
trackDb.sql 2023-12-05 13:53 2.1K
ncbiRefSeqLink.sql 2021-05-13 11:14 2.0K
ncbiRefSeqPredicted.sql 2021-05-13 11:14 2.0K
ncbiRefSeqCurated.sql 2021-05-13 11:14 2.0K
augustusGene.sql 2021-05-13 13:41 2.0K
xenoRefGene.sql 2021-05-18 10:35 2.0K
nestedRepeats.sql 2021-05-12 18:57 2.0K
ncbiRefSeq.sql 2021-05-13 11:14 2.0K
simpleRepeat.sql 2021-05-12 15:31 1.9K
refGene.sql 2021-05-18 10:35 1.9K
rmsk.sql 2021-05-12 18:55 1.9K
mrnaOrientInfo.sql 2021-05-18 12:15 1.8K
estOrientInfo.sql 2021-05-18 12:15 1.8K
hgFindSpec.sql 2023-12-05 13:53 1.8K
xenoRefFlat.sql 2021-05-18 10:36 1.7K
cpgIslandExtUnmasked.sql 2021-05-12 15:00 1.7K
refFlat.sql 2021-05-18 10:35 1.7K
chainMm39.sql 2021-05-18 20:11 1.7K
chainMm10.sql 2021-05-18 09:13 1.7K
chainHg38.sql 2021-05-18 09:29 1.7K
cpgIslandExt.sql 2021-05-13 10:40 1.7K
genscan.sql 2021-05-13 11:26 1.7K
gold.sql 2021-05-12 11:40 1.7K
gap.sql 2021-05-12 11:40 1.6K
history.sql 2021-05-23 08:52 1.6K
seqNcbiRefSeq.sql 2021-05-13 11:16 1.6K
tableList.sql 2024-11-24 03:04 1.6K
chainMm39Link.sql 2021-05-18 20:14 1.6K
chainMm10Link.sql 2021-05-18 09:17 1.6K
chainHg38Link.sql 2021-05-18 09:37 1.6K
cytoBandIdeo.sql 2021-05-13 01:39 1.5K
windowmaskerSdust.sql 2021-05-12 18:25 1.5K
microsat.sql 2021-05-12 16:58 1.5K
extNcbiRefSeq.sql 2021-05-13 11:16 1.5K
ucscToRefSeq.sql 2021-05-13 10:33 1.5K
ucscToINSDC.sql 2021-05-13 10:33 1.4K
chromAlias.sql 2021-05-13 10:21 1.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
chromInfo.sql 2021-05-12 11:40 1.4K
ncbiRefSeqPepTable.sql 2021-05-13 11:16 1.4K
bigFiles.sql 2024-11-24 03:04 1.4K
grp.sql 2021-05-12 11:40 1.4K
ncbiRefSeqCds.sql 2021-05-13 11:16 1.4K
ucscToINSDC.txt.gz 2021-05-13 10:33 1.3K
ucscToRefSeq.txt.gz 2021-05-13 10:33 1.3K
crisprAllTargets.sql 2021-05-23 08:52 1.3K
ncbiRefSeqOther.sql 2021-05-13 11:16 1.3K
gc5BaseBw.sql 2021-05-12 11:40 1.3K
hgFindSpec.txt.gz 2023-12-05 13:53 1.1K
chromInfo.txt.gz 2021-05-12 11:40 1.1K
cytoBandIdeo.txt.gz 2021-05-13 01:39 1.0K
history.txt.gz 2021-05-23 08:52 959
grp.txt.gz 2021-05-12 11:40 213
bigFiles.txt.gz 2024-11-24 03:04 119
extNcbiRefSeq.txt.gz 2021-05-13 11:16 91
ncbiRefSeqOther.txt.gz 2021-05-13 11:16 75
crisprAllTargets.txt.gz 2021-05-23 08:52 69
gc5BaseBw.txt.gz 2021-05-12 11:40 66