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.
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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 -
chainHg38Link.txt.gz 2015-12-21 09:46 1.0G
chainCanFam3Link.txt.gz 2015-12-21 09:41 662M
chainRn6Link.txt.gz 2017-03-26 23:14 630M
chainHg38.txt.gz 2015-12-21 09:44 262M
xenoMrna.txt.gz 2020-08-21 16:55 231M
rmsk.txt.gz 2015-12-21 09:53 137M
windowmaskerSdust.txt.gz 2015-12-21 09:53 132M
chainRn6.txt.gz 2017-03-26 23:00 125M
chainCanFam3.txt.gz 2015-12-21 09:39 107M
netHg38.txt.gz 2015-12-21 09:52 70M
netRn6.txt.gz 2017-03-26 23:42 64M
netCanFam3.txt.gz 2015-12-21 09:52 62M
xenoRefGene.txt.gz 2020-08-21 17:11 27M
xenoRefSeqAli.txt.gz 2020-08-21 17:11 27M
xenoRefFlat.txt.gz 2020-08-21 17:11 25M
simpleRepeat.txt.gz 2015-12-21 09:53 23M
nestedRepeats.txt.gz 2015-12-21 09:51 15M
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:16 10M
ensPep.txt.gz 2018-08-05 06:32 10M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:43 5.0M
ncbiRefSeq.txt.gz 2018-02-09 13:42 3.7M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:42 3.7M
gold.txt.gz 2015-12-21 09:51 3.6M
genscan.txt.gz 2015-12-21 09:51 3.5M
chromAlias.txt.gz 2018-02-04 07:04 3.2M
ensGene.txt.gz 2018-08-05 06:32 2.5M
augustusGene.txt.gz 2015-12-21 09:37 2.3M
cpgIslandExtUnmasked.txt.gz 2015-12-21 09:50 1.8M
ncbiRefSeqLink.txt.gz 2018-02-09 13:42 1.8M
ucscToINSDC.txt.gz 2015-12-21 09:53 1.8M
ucscToRefSeq.txt.gz 2018-02-18 06:29 1.6M
cpgIslandExt.txt.gz 2015-12-21 09:50 1.3M
gap.txt.gz 2015-12-21 09:51 1.3M
microsat.txt.gz 2015-12-21 09:50 1.2M
seqNcbiRefSeq.txt.gz 2018-02-09 14:16 1.1M
chromInfo.txt.gz 2015-12-21 09:50 1.0M
cytoBandIdeo.txt.gz 2015-12-21 09:51 965K
ncbiRefSeqCds.txt.gz 2018-02-09 14:16 366K
ensGtp.txt.gz 2018-08-05 06:32 360K
all_mrna.txt.gz 2020-08-21 16:55 219K
ensemblToGeneName.txt.gz 2018-08-05 06:33 181K
ensemblSource.txt.gz 2018-08-05 06:33 104K
mrnaOrientInfo.txt.gz 2020-08-21 17:11 51K
gbLoaded.txt.gz 2020-08-21 17:17 43K
all_est.txt.gz 2016-05-15 08:39 40K
refSeqAli.txt.gz 2020-08-21 17:11 39K
refGene.txt.gz 2020-08-21 16:55 37K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:42 35K
refFlat.txt.gz 2020-08-21 17:11 35K
trackDb_pushedout.txt.gz 2023-12-05 13:50 32K
trackDb.txt.gz 2023-12-05 13:50 32K
intronEst.txt.gz 2016-05-15 08:39 20K
estOrientInfo.txt.gz 2016-05-15 08:39 14K
tableDescriptions.txt.gz 2024-04-27 02:03 6.4K
tableList.txt.gz 2024-04-28 03:35 3.7K
xenoRefSeqAli.sql 2020-08-21 17:11 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:43 2.1K
refSeqAli.sql 2020-08-21 17:11 2.1K
xenoMrna.sql 2020-08-21 16:55 2.1K
all_mrna.sql 2020-08-21 16:55 2.1K
intronEst.sql 2016-05-15 08:39 2.1K
all_est.sql 2016-05-15 08:39 2.1K
netCanFam3.sql 2015-12-21 09:51 2.1K
netHg38.sql 2015-12-21 09:52 2.1K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
netRn6.sql 2017-03-26 23:40 2.1K
trackDb.sql 2023-12-05 13:50 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:42 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:42 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:42 2.0K
xenoRefGene.sql 2020-08-21 17:11 2.0K
ncbiRefSeq.sql 2018-02-09 13:42 2.0K
refGene.sql 2020-08-21 16:55 1.9K
augustusGene.sql 2015-12-21 09:37 1.9K
nestedRepeats.sql 2015-12-21 09:51 1.9K
simpleRepeat.sql 2015-12-21 09:53 1.9K
ensGene.sql 2018-08-05 06:32 1.9K
rmsk.sql 2015-12-21 09:52 1.9K
mrnaOrientInfo.sql 2020-08-21 17:11 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
estOrientInfo.sql 2016-05-15 08:39 1.8K
hgFindSpec.sql 2023-12-05 13:50 1.8K
xenoRefFlat.sql 2020-08-21 17:11 1.7K
refFlat.sql 2020-08-21 17:11 1.7K
cpgIslandExtUnmasked.sql 2015-12-21 09:50 1.7K
chainCanFam3.sql 2015-12-21 09:39 1.7K
chainHg38.sql 2015-12-21 09:44 1.7K
chainRn6.sql 2017-03-26 22:59 1.7K
cpgIslandExt.sql 2015-12-21 09:50 1.7K
genscan.sql 2015-12-21 09:51 1.7K
gold.sql 2015-12-21 09:51 1.7K
gbLoaded.sql 2020-08-21 17:17 1.6K
gap.sql 2015-12-21 09:51 1.6K
tableList.sql 2024-04-28 03:35 1.6K
history.sql 2015-12-21 09:37 1.6K
seqNcbiRefSeq.sql 2018-02-09 14:16 1.6K
chainCanFam3Link.sql 2015-12-21 09:40 1.5K
chainHg38Link.sql 2015-12-21 09:45 1.5K
chainRn6Link.sql 2017-03-26 23:04 1.5K
cytoBandIdeo.sql 2015-12-21 09:51 1.5K
windowmaskerSdust.sql 2015-12-21 09:53 1.5K
microsat.sql 2015-12-21 09:50 1.5K
extNcbiRefSeq.sql 2018-02-09 14:16 1.5K
tableDescriptions.sql 2024-04-27 02:03 1.5K
ucscToRefSeq.sql 2018-02-18 06:29 1.4K
ucscToINSDC.sql 2015-12-21 09:53 1.4K
chromAlias.sql 2018-02-04 07:04 1.4K
ensGtp.sql 2018-08-05 06:32 1.4K
bigFiles.sql 2024-04-28 03:35 1.4K
ensemblToGeneName.sql 2018-08-05 06:33 1.4K
chromInfo.sql 2015-12-21 09:50 1.4K
ncbiRefSeqPepTable.sql 2018-02-09 14:16 1.4K
ncbiRefSeqCds.sql 2018-02-09 14:16 1.4K
ensemblSource.sql 2018-08-05 06:33 1.4K
grp.sql 2015-12-21 09:51 1.3K
ensPep.sql 2018-08-05 06:32 1.3K
ncbiRefSeqOther.sql 2018-02-09 14:16 1.3K
gc5BaseBw.sql 2015-12-21 09:50 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.3K
hgFindSpec.txt.gz 2023-12-05 13:50 1.3K
history.txt.gz 2015-12-21 09:37 689
grp.txt.gz 2015-12-21 09:51 213
bigFiles.txt.gz 2024-04-28 03:35 95
extNcbiRefSeq.txt.gz 2018-02-09 14:16 91
ncbiRefSeqOther.txt.gz 2018-02-09 14:16 75
gc5BaseBw.txt.gz 2015-12-21 09:50 66