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 -
bigFiles.txt.gz 2024-11-24 03:04 119
bigFiles.sql 2024-11-24 03:04 1.4K
tableList.txt.gz 2024-11-24 03:04 3.2K
tableList.sql 2024-11-24 03:04 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.0K
tableDescriptions.sql 2024-11-23 02:04 1.5K
hgFindSpec.txt.gz 2023-12-05 13:53 1.1K
hgFindSpec.sql 2023-12-05 13:53 1.8K
trackDb.txt.gz 2023-12-05 13:53 31K
trackDb.sql 2023-12-05 13:53 2.1K
history.txt.gz 2021-05-23 08:52 959
history.sql 2021-05-23 08:52 1.6K
crisprAllTargets.txt.gz 2021-05-23 08:52 69
crisprAllTargets.sql 2021-05-23 08:52 1.3K
netMm39.txt.gz 2021-05-18 20:17 58M
netMm39.sql 2021-05-18 20:17 2.1K
chainMm39Link.txt.gz 2021-05-18 20:14 421M
chainMm39Link.sql 2021-05-18 20:14 1.6K
chainMm39.txt.gz 2021-05-18 20:11 48M
chainMm39.sql 2021-05-18 20:11 1.7K
mrnaOrientInfo.txt.gz 2021-05-18 12:15 87K
mrnaOrientInfo.sql 2021-05-18 12:15 1.8K
intronEst.txt.gz 2021-05-18 12:15 8.7M
intronEst.sql 2021-05-18 12:15 2.1K
estOrientInfo.txt.gz 2021-05-18 12:15 4.1M
estOrientInfo.sql 2021-05-18 12:15 1.8K
all_est.txt.gz 2021-05-18 12:15 16M
all_est.sql 2021-05-18 12:15 2.1K
xenoRefSeqAli.txt.gz 2021-05-18 10:36 21M
xenoRefSeqAli.sql 2021-05-18 10:36 2.1K
refSeqAli.txt.gz 2021-05-18 10:36 185K
refSeqAli.sql 2021-05-18 10:36 2.1K
xenoRefFlat.txt.gz 2021-05-18 10:36 10M
xenoRefFlat.sql 2021-05-18 10:36 1.7K
xenoRefGene.txt.gz 2021-05-18 10:35 11M
xenoRefGene.sql 2021-05-18 10:35 2.0K
refFlat.txt.gz 2021-05-18 10:35 165K
refFlat.sql 2021-05-18 10:35 1.7K
refGene.txt.gz 2021-05-18 10:35 178K
refGene.sql 2021-05-18 10:35 1.9K
xenoMrna.txt.gz 2021-05-18 10:08 218M
xenoMrna.sql 2021-05-18 10:08 2.1K
all_mrna.txt.gz 2021-05-18 10:07 221K
all_mrna.sql 2021-05-18 10:07 2.1K
netHg38.txt.gz 2021-05-18 09:40 63M
netHg38.sql 2021-05-18 09:40 2.1K
chainHg38Link.txt.gz 2021-05-18 09:37 914M
chainHg38Link.sql 2021-05-18 09:37 1.6K
chainHg38.txt.gz 2021-05-18 09:29 211M
chainHg38.sql 2021-05-18 09:29 1.7K
netMm10.txt.gz 2021-05-18 09:20 58M
netMm10.sql 2021-05-18 09:20 2.1K
chainMm10Link.txt.gz 2021-05-18 09:17 455M
chainMm10Link.sql 2021-05-18 09:17 1.6K
chainMm10.txt.gz 2021-05-18 09:13 55M
chainMm10.sql 2021-05-18 09:13 1.7K
augustusGene.txt.gz 2021-05-13 13:41 2.2M
augustusGene.sql 2021-05-13 13:41 2.0K
genscan.txt.gz 2021-05-13 11:26 2.9M
genscan.sql 2021-05-13 11:26 1.7K
ncbiRefSeqPepTable.txt.gz 2021-05-13 11:16 12M
ncbiRefSeqPepTable.sql 2021-05-13 11:16 1.4K
ncbiRefSeqCds.txt.gz 2021-05-13 11:16 433K
ncbiRefSeqCds.sql 2021-05-13 11:16 1.4K
extNcbiRefSeq.txt.gz 2021-05-13 11:16 91
extNcbiRefSeq.sql 2021-05-13 11:16 1.5K
seqNcbiRefSeq.txt.gz 2021-05-13 11:16 1.4M
seqNcbiRefSeq.sql 2021-05-13 11:16 1.6K
ncbiRefSeqOther.txt.gz 2021-05-13 11:16 75
ncbiRefSeqOther.sql 2021-05-13 11:16 1.3K
ncbiRefSeqPsl.txt.gz 2021-05-13 11:14 6.1M
ncbiRefSeqPsl.sql 2021-05-13 11:14 2.1K
ncbiRefSeqLink.txt.gz 2021-05-13 11:14 2.4M
ncbiRefSeqLink.sql 2021-05-13 11:14 2.0K
ncbiRefSeqPredicted.txt.gz 2021-05-13 11:14 4.1M
ncbiRefSeqPredicted.sql 2021-05-13 11:14 2.0K
ncbiRefSeqCurated.txt.gz 2021-05-13 11:14 184K
ncbiRefSeqCurated.sql 2021-05-13 11:14 2.0K
ncbiRefSeq.txt.gz 2021-05-13 11:14 4.3M
ncbiRefSeq.sql 2021-05-13 11:14 2.0K
cpgIslandExt.txt.gz 2021-05-13 10:40 1.0M
cpgIslandExt.sql 2021-05-13 10:40 1.7K
ucscToRefSeq.txt.gz 2021-05-13 10:33 1.3K
ucscToRefSeq.sql 2021-05-13 10:33 1.5K
ucscToINSDC.txt.gz 2021-05-13 10:33 1.3K
ucscToINSDC.sql 2021-05-13 10:33 1.4K
chromAlias.txt.gz 2021-05-13 10:21 2.2K
chromAlias.sql 2021-05-13 10:21 1.4K
cytoBandIdeo.txt.gz 2021-05-13 01:39 1.0K
cytoBandIdeo.sql 2021-05-13 01:39 1.5K
nestedRepeats.txt.gz 2021-05-12 18:57 14M
nestedRepeats.sql 2021-05-12 18:57 2.0K
rmsk.txt.gz 2021-05-12 18:55 121M
rmsk.sql 2021-05-12 18:55 1.9K
windowmaskerSdust.txt.gz 2021-05-12 18:25 123M
windowmaskerSdust.sql 2021-05-12 18:25 1.5K
microsat.txt.gz 2021-05-12 16:58 576K
microsat.sql 2021-05-12 16:58 1.5K
simpleRepeat.txt.gz 2021-05-12 15:31 22M
simpleRepeat.sql 2021-05-12 15:31 1.9K
cpgIslandExtUnmasked.txt.gz 2021-05-12 15:00 1.1M
cpgIslandExtUnmasked.sql 2021-05-12 15:00 1.7K
grp.txt.gz 2021-05-12 11:40 213
grp.sql 2021-05-12 11:40 1.4K
chromInfo.txt.gz 2021-05-12 11:40 1.1K
chromInfo.sql 2021-05-12 11:40 1.4K
gc5BaseBw.txt.gz 2021-05-12 11:40 66
gc5BaseBw.sql 2021-05-12 11:40 1.3K
gap.txt.gz 2021-05-12 11:40 13K
gap.sql 2021-05-12 11:40 1.6K
gold.txt.gz 2021-05-12 11:40 22K
gold.sql 2021-05-12 11:40 1.7K