This directory contains a dump of the UCSC genome annotation database for the
Apr. 2011 (MusPutFur1.0/musFur1) assembly of the ferret genome
(musFur1, Ferret Genome Sequencing Consortium) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/3295
http://www.ncbi.nlm.nih.gov/genome/assembly/286418
http://www.ncbi.nlm.nih.gov/bioproject/59869
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=musFur1
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.cse.ucsc.edu, then go to
the directory goldenPath/musFur1/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.cse.ucsc.edu/goldenPath/musFur1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/musFur1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/musFur1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/musFur1/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
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 musFur1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql musFur1 --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 -
simpleRepeat.sql 2013-06-10 15:07 1.9K
simpleRepeat.txt.gz 2013-06-10 15:07 15M
cpgIslandExt.sql 2013-06-10 15:08 1.7K
cpgIslandExt.txt.gz 2013-06-10 15:08 1.1M
chromInfo.sql 2013-06-10 15:08 1.4K
chromInfo.txt.gz 2013-06-10 15:08 29K
rmsk.sql 2013-06-10 15:09 1.9K
rmsk.txt.gz 2013-06-10 15:09 109M
intronEst.sql 2013-06-10 15:09 2.1K
history.sql 2013-06-10 15:09 1.6K
history.txt.gz 2013-06-10 15:09 389
intronEst.txt.gz 2013-06-10 15:09 224K
genscan.sql 2013-06-10 15:09 1.7K
genscan.txt.gz 2013-06-10 15:09 3.1M
gap.sql 2013-06-10 15:09 1.6K
gap.txt.gz 2013-06-10 15:09 1.5M
ucscToEnsembl.sql 2013-06-10 15:09 1.4K
ucscToEnsembl.txt.gz 2013-06-10 15:09 37K
all_est.sql 2013-06-10 15:10 2.1K
all_est.txt.gz 2013-06-10 15:10 289K
gc5BaseBw.sql 2013-06-10 15:10 1.3K
gc5BaseBw.txt.gz 2013-06-10 15:10 63
windowmaskerSdust.sql 2013-06-10 15:10 1.5K
windowmaskerSdust.txt.gz 2013-06-10 15:10 123M
nestedRepeats.sql 2013-06-10 15:10 1.9K
nestedRepeats.txt.gz 2013-06-10 15:10 11M
gold.sql 2013-06-10 15:10 1.7K
estOrientInfo.sql 2013-06-10 15:10 1.8K
estOrientInfo.txt.gz 2013-06-10 15:10 51K
gold.txt.gz 2013-06-10 15:10 1.9M
ucscToINSDC.sql 2013-09-15 16:46 1.4K
ucscToINSDC.txt.gz 2013-09-15 16:46 49K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 17:04 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:04 1.1M
cytoBandIdeo.sql 2014-10-19 13:36 1.5K
cytoBandIdeo.txt.gz 2014-10-19 13:36 28K
xenoMrna.sql 2015-03-02 19:49 2.1K
xenoMrna.txt.gz 2015-03-02 19:49 33
augustusGene.sql 2015-07-26 16:47 1.9K
augustusGene.txt.gz 2015-07-26 16:47 2.3M
microsat.sql 2015-08-23 21:57 1.5K
microsat.txt.gz 2015-08-23 21:57 319K
chromAlias.sql 2018-08-05 08:19 1.4K
chromAlias.txt.gz 2018-08-05 08:19 36K
refSeqAli.sql 2019-03-17 11:28 2.1K
refSeqAli.txt.gz 2019-03-17 11:28 5.9K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 1.0K
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.5M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:28 3.1M
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 330K
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.9M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 3.1M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 4.1M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 855K
all_mrna.sql 2020-08-19 18:55 2.1K
all_mrna.txt.gz 2020-08-19 18:55 5.9M
mrnaOrientInfo.sql 2020-08-19 18:55 1.8K
mrnaOrientInfo.txt.gz 2020-08-19 18:55 1.6M
refGene.sql 2020-08-19 18:55 1.9K
refGene.txt.gz 2020-08-19 18:55 5.6K
refFlat.sql 2020-08-19 18:55 1.7K
refFlat.txt.gz 2020-08-19 18:55 5.0K
xenoRefGene.sql 2020-08-19 19:21 2.0K
xenoRefGene.txt.gz 2020-08-19 19:21 32M
xenoRefFlat.sql 2020-08-19 19:23 1.7K
xenoRefFlat.txt.gz 2020-08-19 19:23 30M
xenoRefSeqAli.sql 2020-08-19 19:23 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 19:23 33M
gbLoaded.sql 2020-08-19 19:23 1.6K
gbLoaded.txt.gz 2020-08-19 19:23 77K
ensGene.sql 2021-05-25 14:38 1.9K
ensGene.txt.gz 2021-05-25 14:38 2.4M
ensGtp.sql 2021-05-25 14:38 1.4K
ensGtp.txt.gz 2021-05-25 14:38 291K
ensemblToGeneName.sql 2021-05-25 14:38 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:38 122K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 87K
ensPep.sql 2021-05-25 14:41 1.3K
ensPep.txt.gz 2021-05-25 14:41 6.0M
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 22K
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 5.8K
tableList.sql 2024-11-17 03:38 1.6K
tableList.txt.gz 2024-11-17 03:38 3.0K
bigFiles.sql 2024-11-17 03:38 1.4K
bigFiles.txt.gz 2024-11-17 03:38 94