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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-05-05 21:19 22M
xenoRefSeqAli.sql 2020-05-05 21:19 2.1K
xenoRefGene.txt.gz 2020-05-05 21:19 12M
xenoRefGene.sql 2020-05-05 21:19 2.0K
xenoRefFlat.txt.gz 2020-05-05 21:19 11M
xenoRefFlat.sql 2020-05-05 21:19 1.7K
xenoMrna.txt.gz 2020-05-05 20:50 223M
xenoMrna.sql 2020-05-05 20:50 2.1K
windowmaskerSdust.txt.gz 2020-03-31 17:05 125M
windowmaskerSdust.sql 2020-03-31 17:05 1.5K
uuGene.txt.gz 2020-09-08 15:09 8.4M
uuGene.sql 2020-09-08 15:09 1.8K
ucscToINSDC.txt.gz 2020-04-02 11:42 19K
ucscToINSDC.sql 2020-04-02 11:42 1.4K
trackDb.txt.gz 2024-01-31 15:13 36K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-24 03:04 3.6K
tableList.sql 2024-11-24 03:04 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.4K
tableDescriptions.sql 2024-11-23 02:04 1.4K
structVar.txt.gz 2020-09-08 15:26 1.8M
structVar.sql 2020-09-08 15:26 1.5K
simpleRepeat.txt.gz 2020-03-31 12:19 27M
simpleRepeat.sql 2020-03-31 12:19 1.9K
seqNcbiRefSeq.txt.gz 2022-01-26 15:08 1.4M
seqNcbiRefSeq.sql 2022-01-26 15:08 1.6K
rmsk.txt.gz 2020-03-31 15:40 128M
rmsk.sql 2020-03-31 15:40 1.9K
refSeqAli.txt.gz 2020-05-05 21:19 189K
refSeqAli.sql 2020-05-05 21:19 2.1K
refGene.txt.gz 2020-05-05 21:19 182K
refGene.sql 2020-05-05 21:19 1.9K
refFlat.txt.gz 2020-05-05 21:19 169K
refFlat.sql 2020-05-05 21:19 1.7K
netNeoSch1.txt.gz 2020-07-13 23:11 56M
netNeoSch1.sql 2020-07-13 23:11 2.1K
netMm10.txt.gz 2020-04-09 15:51 60M
netMm10.sql 2020-04-09 15:51 2.1K
netHg38.txt.gz 2020-04-09 16:25 66M
netHg38.sql 2020-04-09 16:25 2.1K
netCanFam3.txt.gz 2020-05-13 11:07 5.6M
netCanFam3.sql 2020-05-13 11:07 2.1K
nestedRepeats.txt.gz 2020-03-31 15:42 15M
nestedRepeats.sql 2020-03-31 15:42 2.0K
ncbiRefSeqPsl.txt.gz 2022-01-26 15:04 6.1M
ncbiRefSeqPsl.sql 2022-01-26 15:04 2.1K
ncbiRefSeqPredicted.txt.gz 2022-01-26 15:04 4.1M
ncbiRefSeqPredicted.sql 2022-01-26 15:04 2.0K
ncbiRefSeqPepTable.txt.gz 2022-01-26 15:08 7.4M
ncbiRefSeqPepTable.sql 2022-01-26 15:08 1.4K
ncbiRefSeqOther.txt.gz 2022-01-26 15:08 75
ncbiRefSeqOther.sql 2022-01-26 15:08 1.3K
ncbiRefSeqLink.txt.gz 2022-01-26 15:04 2.1M
ncbiRefSeqLink.sql 2022-01-26 15:04 2.0K
ncbiRefSeqCurated.txt.gz 2022-01-26 15:04 190K
ncbiRefSeqCurated.sql 2022-01-26 15:04 2.0K
ncbiRefSeqCds.txt.gz 2022-01-26 15:08 427K
ncbiRefSeqCds.sql 2022-01-26 15:08 1.4K
ncbiRefSeq.txt.gz 2022-01-26 15:04 4.3M
ncbiRefSeq.sql 2022-01-26 15:04 2.0K
mrnaOrientInfo.txt.gz 2020-05-06 00:55 88K
mrnaOrientInfo.sql 2020-05-06 00:55 1.8K
microsat.txt.gz 2020-03-31 15:38 672K
microsat.sql 2020-03-31 15:38 1.5K
miRNA.txt.gz 2020-09-09 16:31 18K
miRNA.sql 2020-09-09 16:31 1.7K
intronEst.txt.gz 2020-05-06 00:36 8.9M
intronEst.sql 2020-05-06 00:36 2.1K
history.txt.gz 2020-05-20 11:32 815
history.sql 2020-05-20 11:32 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.1K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2020-03-31 11:00 213
grp.sql 2020-03-31 11:00 1.4K
gold.txt.gz 2020-03-31 10:33 37K
gold.sql 2020-03-31 10:33 1.7K
genscan.txt.gz 2020-04-09 15:57 3.1M
genscan.sql 2020-04-09 15:57 1.7K
gc5BaseBw.txt.gz 2020-03-31 11:00 66
gc5BaseBw.sql 2020-03-31 11:00 1.3K
gbLoaded.txt.gz 2020-05-06 00:55 1.4K
gbLoaded.sql 2020-05-06 00:55 1.6K
gap.txt.gz 2020-03-31 10:33 7.2K
gap.sql 2020-03-31 10:33 1.6K
extNcbiRefSeq.txt.gz 2022-01-26 15:08 91
extNcbiRefSeq.sql 2022-01-26 15:08 1.5K
estOrientInfo.txt.gz 2020-05-06 00:36 4.5M
estOrientInfo.sql 2020-05-06 00:36 1.8K
cytoBandIdeo.txt.gz 2020-03-31 11:00 13K
cytoBandIdeo.sql 2020-03-31 11:00 1.5K
crisprAllTargets.txt.gz 2020-04-16 02:07 69
crisprAllTargets.sql 2020-04-16 02:07 1.3K
cpgIslandExtUnmasked.txt.gz 2020-03-31 10:56 1.1M
cpgIslandExtUnmasked.sql 2020-03-31 10:56 1.7K
cpgIslandExt.txt.gz 2020-04-02 09:50 1.0M
cpgIslandExt.sql 2020-04-02 09:50 1.7K
chromInfo.txt.gz 2020-03-31 11:02 14K
chromInfo.sql 2020-03-31 11:02 1.4K
chromAlias.txt.gz 2020-05-20 10:44 12K
chromAlias.sql 2020-05-20 10:44 1.4K
chainNeoSch1Link.txt.gz 2020-07-13 23:03 1.9G
chainNeoSch1Link.sql 2020-07-13 23:03 1.6K
chainNeoSch1.txt.gz 2020-07-13 22:45 408M
chainNeoSch1.sql 2020-07-13 22:45 1.7K
chainMm10Link.txt.gz 2020-04-09 15:43 474M
chainMm10Link.sql 2020-04-09 15:43 1.6K
chainMm10.txt.gz 2020-04-09 15:40 58M
chainMm10.sql 2020-04-09 15:40 1.7K
chainHg38Link.txt.gz 2020-04-09 16:17 1.2G
chainHg38Link.sql 2020-04-09 16:17 1.6K
chainHg38.txt.gz 2020-04-09 16:05 408M
chainHg38.sql 2020-04-09 16:05 1.7K
chainCanFam3Link.txt.gz 2020-05-13 10:59 6.4G
chainCanFam3Link.sql 2020-05-13 10:59 1.6K
chainCanFam3.txt.gz 2020-05-13 09:53 734M
chainCanFam3.sql 2020-05-13 09:53 1.7K
bigFiles.txt.gz 2024-11-24 03:04 175
bigFiles.sql 2024-11-24 03:04 1.4K
augustusGene.txt.gz 2020-04-10 10:30 2.3M
augustusGene.sql 2020-04-10 10:30 2.0K
altAllele.txt.gz 2020-09-08 16:34 112
altAllele.sql 2020-09-08 16:34 1.3K
all_mrna.txt.gz 2020-05-05 20:49 224K
all_mrna.sql 2020-05-05 20:49 2.1K
all_est.txt.gz 2020-05-06 00:36 17M
all_est.sql 2020-05-06 00:36 2.1K