This directory contains a dump of the UCSC genome annotation database for the
Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) assembly of the dog genome
(canFam4, Uppsala University) .
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/6119491
https://www.ncbi.nlm.nih.gov/bioproject/587469
https://www.ncbi.nlm.nih.gov/biosample/SAMN13230619
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=canFam4
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/canFam4/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/canFam4/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/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 canFam4 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql canFam4 --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 -
gc5BaseBw.txt.gz 2020-03-31 11:00 66
crisprAllTargets.txt.gz 2020-04-16 02:07 69
ncbiRefSeqOther.txt.gz 2022-01-26 15:08 75
extNcbiRefSeq.txt.gz 2022-01-26 15:08 91
altAllele.txt.gz 2020-09-08 16:34 112
bigFiles.txt.gz 2024-11-17 03:14 175
grp.txt.gz 2020-03-31 11:00 213
history.txt.gz 2020-05-20 11:32 815
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
altAllele.sql 2020-09-08 16:34 1.3K
gc5BaseBw.sql 2020-03-31 11:00 1.3K
ncbiRefSeqOther.sql 2022-01-26 15:08 1.3K
crisprAllTargets.sql 2020-04-16 02:07 1.3K
ncbiRefSeqCds.sql 2022-01-26 15:08 1.4K
grp.sql 2020-03-31 11:00 1.4K
bigFiles.sql 2024-11-17 03:14 1.4K
ncbiRefSeqPepTable.sql 2022-01-26 15:08 1.4K
chromInfo.sql 2020-03-31 11:02 1.4K
gbLoaded.txt.gz 2020-05-06 00:55 1.4K
tableDescriptions.sql 2024-11-16 02:04 1.4K
chromAlias.sql 2020-05-20 10:44 1.4K
ucscToINSDC.sql 2020-04-02 11:42 1.4K
extNcbiRefSeq.sql 2022-01-26 15:08 1.5K
microsat.sql 2020-03-31 15:38 1.5K
structVar.sql 2020-09-08 15:26 1.5K
windowmaskerSdust.sql 2020-03-31 17:05 1.5K
cytoBandIdeo.sql 2020-03-31 11:00 1.5K
chainHg38Link.sql 2020-04-09 16:17 1.6K
chainMm10Link.sql 2020-04-09 15:43 1.6K
tableList.sql 2024-11-17 03:14 1.6K
seqNcbiRefSeq.sql 2022-01-26 15:08 1.6K
chainCanFam3Link.sql 2020-05-13 10:59 1.6K
chainNeoSch1Link.sql 2020-07-13 23:03 1.6K
history.sql 2020-05-20 11:32 1.6K
gbLoaded.sql 2020-05-06 00:55 1.6K
gap.sql 2020-03-31 10:33 1.6K
gold.sql 2020-03-31 10:33 1.7K
genscan.sql 2020-04-09 15:57 1.7K
miRNA.sql 2020-09-09 16:31 1.7K
cpgIslandExt.sql 2020-04-02 09:50 1.7K
chainHg38.sql 2020-04-09 16:05 1.7K
chainMm10.sql 2020-04-09 15:40 1.7K
refFlat.sql 2020-05-05 21:19 1.7K
chainCanFam3.sql 2020-05-13 09:53 1.7K
chainNeoSch1.sql 2020-07-13 22:45 1.7K
cpgIslandExtUnmasked.sql 2020-03-31 10:56 1.7K
xenoRefFlat.sql 2020-05-05 21:19 1.7K
hgFindSpec.sql 2024-01-31 15:13 1.8K
uuGene.sql 2020-09-08 15:09 1.8K
estOrientInfo.sql 2020-05-06 00:36 1.8K
mrnaOrientInfo.sql 2020-05-06 00:55 1.8K
rmsk.sql 2020-03-31 15:40 1.9K
refGene.sql 2020-05-05 21:19 1.9K
simpleRepeat.sql 2020-03-31 12:19 1.9K
ncbiRefSeq.sql 2022-01-26 15:04 2.0K
nestedRepeats.sql 2020-03-31 15:42 2.0K
xenoRefGene.sql 2020-05-05 21:19 2.0K
augustusGene.sql 2020-04-10 10:30 2.0K
ncbiRefSeqCurated.sql 2022-01-26 15:04 2.0K
ncbiRefSeqPredicted.sql 2022-01-26 15:04 2.0K
ncbiRefSeqLink.sql 2022-01-26 15:04 2.0K
trackDb.sql 2024-01-31 15:13 2.1K
netHg38.sql 2020-04-09 16:25 2.1K
netMm10.sql 2020-04-09 15:51 2.1K
netCanFam3.sql 2020-05-13 11:07 2.1K
netNeoSch1.sql 2020-07-13 23:11 2.1K
all_est.sql 2020-05-06 00:36 2.1K
all_mrna.sql 2020-05-05 20:49 2.1K
xenoMrna.sql 2020-05-05 20:50 2.1K
intronEst.sql 2020-05-06 00:36 2.1K
refSeqAli.sql 2020-05-05 21:19 2.1K
ncbiRefSeqPsl.sql 2022-01-26 15:04 2.1K
xenoRefSeqAli.sql 2020-05-05 21:19 2.1K
tableList.txt.gz 2024-11-17 03:14 3.6K
tableDescriptions.txt.gz 2024-11-16 02:04 6.4K
gap.txt.gz 2020-03-31 10:33 7.2K
chromAlias.txt.gz 2020-05-20 10:44 12K
cytoBandIdeo.txt.gz 2020-03-31 11:00 13K
chromInfo.txt.gz 2020-03-31 11:02 14K
miRNA.txt.gz 2020-09-09 16:31 18K
ucscToINSDC.txt.gz 2020-04-02 11:42 19K
trackDb.txt.gz 2024-01-31 15:13 36K
gold.txt.gz 2020-03-31 10:33 37K
mrnaOrientInfo.txt.gz 2020-05-06 00:55 88K
refFlat.txt.gz 2020-05-05 21:19 169K
refGene.txt.gz 2020-05-05 21:19 182K
refSeqAli.txt.gz 2020-05-05 21:19 189K
ncbiRefSeqCurated.txt.gz 2022-01-26 15:04 190K
all_mrna.txt.gz 2020-05-05 20:49 224K
ncbiRefSeqCds.txt.gz 2022-01-26 15:08 427K
microsat.txt.gz 2020-03-31 15:38 672K
cpgIslandExt.txt.gz 2020-04-02 09:50 1.0M
cpgIslandExtUnmasked.txt.gz 2020-03-31 10:56 1.1M
seqNcbiRefSeq.txt.gz 2022-01-26 15:08 1.4M
structVar.txt.gz 2020-09-08 15:26 1.8M
ncbiRefSeqLink.txt.gz 2022-01-26 15:04 2.1M
augustusGene.txt.gz 2020-04-10 10:30 2.3M
genscan.txt.gz 2020-04-09 15:57 3.1M
ncbiRefSeqPredicted.txt.gz 2022-01-26 15:04 4.1M
ncbiRefSeq.txt.gz 2022-01-26 15:04 4.3M
estOrientInfo.txt.gz 2020-05-06 00:36 4.5M
netCanFam3.txt.gz 2020-05-13 11:07 5.6M
ncbiRefSeqPsl.txt.gz 2022-01-26 15:04 6.1M
ncbiRefSeqPepTable.txt.gz 2022-01-26 15:08 7.4M
uuGene.txt.gz 2020-09-08 15:09 8.4M
intronEst.txt.gz 2020-05-06 00:36 8.9M
xenoRefFlat.txt.gz 2020-05-05 21:19 11M
xenoRefGene.txt.gz 2020-05-05 21:19 12M
nestedRepeats.txt.gz 2020-03-31 15:42 15M
all_est.txt.gz 2020-05-06 00:36 17M
xenoRefSeqAli.txt.gz 2020-05-05 21:19 22M
simpleRepeat.txt.gz 2020-03-31 12:19 27M
netNeoSch1.txt.gz 2020-07-13 23:11 56M
chainMm10.txt.gz 2020-04-09 15:40 58M
netMm10.txt.gz 2020-04-09 15:51 60M
netHg38.txt.gz 2020-04-09 16:25 66M
windowmaskerSdust.txt.gz 2020-03-31 17:05 125M
rmsk.txt.gz 2020-03-31 15:40 128M
xenoMrna.txt.gz 2020-05-05 20:50 223M
chainNeoSch1.txt.gz 2020-07-13 22:45 408M
chainHg38.txt.gz 2020-04-09 16:05 408M
chainMm10Link.txt.gz 2020-04-09 15:43 474M
chainCanFam3.txt.gz 2020-05-13 09:53 734M
chainHg38Link.txt.gz 2020-04-09 16:17 1.2G
chainNeoSch1Link.txt.gz 2020-07-13 23:03 1.9G
chainCanFam3Link.txt.gz 2020-05-13 10:59 6.4G