This directory contains a dump of the UCSC genome annotation database for the
Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) assembly of the cat genome
(felCat8, International Cat 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/78
http://www.ncbi.nlm.nih.gov/genome/assembly/1373248
http://www.ncbi.nlm.nih.gov/bioproject/16726
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=felCat8
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/felCat8/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/felCat8/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/felCat8/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat8/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat8/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 felCat8 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql felCat8 --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 2020-08-21 17:11 27M
xenoRefSeqAli.sql 2020-08-21 17:11 2.1K
xenoRefGene.txt.gz 2020-08-21 17:11 27M
xenoRefGene.sql 2020-08-21 17:11 2.0K
xenoRefFlat.txt.gz 2020-08-21 17:11 25M
xenoRefFlat.sql 2020-08-21 17:11 1.7K
xenoMrna.txt.gz 2020-08-21 16:55 231M
xenoMrna.sql 2020-08-21 16:55 2.1K
windowmaskerSdust.txt.gz 2015-12-21 09:53 132M
windowmaskerSdust.sql 2015-12-21 09:53 1.5K
ucscToRefSeq.txt.gz 2018-02-18 06:29 1.6M
ucscToRefSeq.sql 2018-02-18 06:29 1.4K
ucscToINSDC.txt.gz 2015-12-21 09:53 1.8M
ucscToINSDC.sql 2015-12-21 09:53 1.4K
trackDb.txt.gz 2024-07-25 09:34 60K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-17 03:38 3.5K
tableList.sql 2024-11-17 03:38 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
simpleRepeat.txt.gz 2015-12-21 09:53 23M
simpleRepeat.sql 2015-12-21 09:53 1.9K
seqNcbiRefSeq.txt.gz 2018-02-09 14:16 1.1M
seqNcbiRefSeq.sql 2018-02-09 14:16 1.6K
rmsk.txt.gz 2015-12-21 09:53 137M
rmsk.sql 2015-12-21 09:52 1.9K
refSeqAli.txt.gz 2020-08-21 17:11 39K
refSeqAli.sql 2020-08-21 17:11 2.1K
refGene.txt.gz 2020-08-21 16:55 37K
refGene.sql 2020-08-21 16:55 1.9K
refFlat.txt.gz 2020-08-21 17:11 35K
refFlat.sql 2020-08-21 17:11 1.7K
netRn6.txt.gz 2017-03-26 23:42 64M
netRn6.sql 2017-03-26 23:40 2.1K
netHg38.txt.gz 2015-12-21 09:52 70M
netHg38.sql 2015-12-21 09:52 2.1K
netCanFam3.txt.gz 2015-12-21 09:52 62M
netCanFam3.sql 2015-12-21 09:51 2.1K
nestedRepeats.txt.gz 2015-12-21 09:51 15M
nestedRepeats.sql 2015-12-21 09:51 1.9K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:43 5.0M
ncbiRefSeqPsl.sql 2018-02-09 13:43 2.1K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:42 3.7M
ncbiRefSeqPredicted.sql 2018-02-09 13:42 2.0K
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:16 10M
ncbiRefSeqPepTable.sql 2018-02-09 14:16 1.4K
ncbiRefSeqOther.txt.gz 2018-02-09 14:16 75
ncbiRefSeqOther.sql 2018-02-09 14:16 1.3K
ncbiRefSeqLink.txt.gz 2018-02-09 13:42 1.8M
ncbiRefSeqLink.sql 2018-02-09 13:42 2.0K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:42 35K
ncbiRefSeqCurated.sql 2018-02-09 13:42 2.0K
ncbiRefSeqCds.txt.gz 2018-02-09 14:16 366K
ncbiRefSeqCds.sql 2018-02-09 14:16 1.4K
ncbiRefSeq.txt.gz 2018-02-09 13:42 3.7M
ncbiRefSeq.sql 2018-02-09 13:42 2.0K
mrnaOrientInfo.txt.gz 2020-08-21 17:11 51K
mrnaOrientInfo.sql 2020-08-21 17:11 1.8K
microsat.txt.gz 2015-12-21 09:50 1.2M
microsat.sql 2015-12-21 09:50 1.5K
intronEst.txt.gz 2016-05-15 08:39 20K
intronEst.sql 2016-05-15 08:39 2.1K
history.txt.gz 2015-12-21 09:37 689
history.sql 2015-12-21 09:37 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
grp.txt.gz 2015-12-21 09:51 213
grp.sql 2015-12-21 09:51 1.3K
gold.txt.gz 2015-12-21 09:51 3.6M
gold.sql 2015-12-21 09:51 1.7K
genscan.txt.gz 2015-12-21 09:51 3.5M
genscan.sql 2015-12-21 09:51 1.7K
gc5BaseBw.txt.gz 2015-12-21 09:50 66
gc5BaseBw.sql 2015-12-21 09:50 1.3K
gbLoaded.txt.gz 2020-08-21 17:17 43K
gbLoaded.sql 2020-08-21 17:17 1.6K
gap.txt.gz 2015-12-21 09:51 1.3M
gap.sql 2015-12-21 09:51 1.6K
extNcbiRefSeq.txt.gz 2018-02-09 14:16 91
extNcbiRefSeq.sql 2018-02-09 14:16 1.5K
estOrientInfo.txt.gz 2016-05-15 08:39 14K
estOrientInfo.sql 2016-05-15 08:39 1.8K
ensemblToGeneName.txt.gz 2018-08-05 06:33 181K
ensemblToGeneName.sql 2018-08-05 06:33 1.4K
ensemblSource.txt.gz 2018-08-05 06:33 104K
ensemblSource.sql 2018-08-05 06:33 1.4K
ensPep.txt.gz 2018-08-05 06:32 10M
ensPep.sql 2018-08-05 06:32 1.3K
ensGtp.txt.gz 2018-08-05 06:32 360K
ensGtp.sql 2018-08-05 06:32 1.4K
ensGene.txt.gz 2018-08-05 06:32 2.5M
ensGene.sql 2018-08-05 06:32 1.9K
cytoBandIdeo.txt.gz 2015-12-21 09:51 965K
cytoBandIdeo.sql 2015-12-21 09:51 1.5K
cpgIslandExtUnmasked.txt.gz 2015-12-21 09:50 1.8M
cpgIslandExtUnmasked.sql 2015-12-21 09:50 1.7K
cpgIslandExt.txt.gz 2015-12-21 09:50 1.3M
cpgIslandExt.sql 2015-12-21 09:50 1.7K
chromInfo.txt.gz 2015-12-21 09:50 1.0M
chromInfo.sql 2015-12-21 09:50 1.4K
chromAlias.txt.gz 2018-02-04 07:04 3.2M
chromAlias.sql 2018-02-04 07:04 1.4K
chainRn6Link.txt.gz 2017-03-26 23:14 630M
chainRn6Link.sql 2017-03-26 23:04 1.5K
chainRn6.txt.gz 2017-03-26 23:00 125M
chainRn6.sql 2017-03-26 22:59 1.7K
chainHg38Link.txt.gz 2015-12-21 09:46 1.0G
chainHg38Link.sql 2015-12-21 09:45 1.5K
chainHg38.txt.gz 2015-12-21 09:44 262M
chainHg38.sql 2015-12-21 09:44 1.7K
chainCanFam3Link.txt.gz 2015-12-21 09:41 662M
chainCanFam3Link.sql 2015-12-21 09:40 1.5K
chainCanFam3.txt.gz 2015-12-21 09:39 107M
chainCanFam3.sql 2015-12-21 09:39 1.7K
bigFiles.txt.gz 2024-11-17 03:38 95
bigFiles.sql 2024-11-17 03:38 1.4K
augustusGene.txt.gz 2015-12-21 09:37 2.3M
augustusGene.sql 2015-12-21 09:37 1.9K
all_mrna.txt.gz 2020-08-21 16:55 219K
all_mrna.sql 2020-08-21 16:55 2.1K
all_est.txt.gz 2016-05-15 08:39 40K
all_est.sql 2016-05-15 08:39 2.1K