This directory contains a dump of the UCSC genome annotation database for
the Sep. 2011 (ICGSC Felis_catus 6.2/felCat5) assembly of the cat genome
(felCat5, International Cat Genome Sequencing Consortium Felis_catus-6.2
(NCBI project 16726, accession AANG00000000.2, GCA_000181335.2)).
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/320798
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=felCat5
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/felCat5/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/felCat5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/felCat5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/felCat5/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 felCat5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql felCat5 --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.
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Name Last modified Size Description
Parent Directory -
simpleRepeat.sql 2012-11-21 14:10 1.9K
simpleRepeat.txt.gz 2012-11-21 14:10 19M
chainMm10.sql 2012-11-21 14:10 1.7K
chainMm10.txt.gz 2012-11-21 14:10 50M
cpgIslandExt.sql 2012-11-21 14:11 1.7K
cpgIslandExt.txt.gz 2012-11-21 14:11 1.2M
all_est.sql 2012-11-21 14:11 2.1K
all_est.txt.gz 2012-11-21 14:11 40K
estOrientInfo.sql 2012-11-21 14:12 1.8K
estOrientInfo.txt.gz 2012-11-21 14:12 14K
rmsk.sql 2012-11-21 14:12 1.9K
rmsk.txt.gz 2012-11-21 14:12 120M
windowmaskerSdust.sql 2012-11-21 14:12 1.5K
windowmaskerSdust.txt.gz 2012-11-21 14:13 125M
gc5BaseBw.sql 2012-11-21 14:13 1.3K
gc5BaseBw.txt.gz 2012-11-21 14:13 63
nestedRepeats.sql 2012-11-21 14:13 1.9K
nestedRepeats.txt.gz 2012-11-21 14:13 14M
chromInfo.sql 2012-11-21 14:16 1.4K
chromInfo.txt.gz 2012-11-21 14:16 29K
history.sql 2012-11-21 14:16 1.6K
history.txt.gz 2012-11-21 14:16 514
genscan.sql 2012-11-21 14:16 1.7K
genscan.txt.gz 2012-11-21 14:16 3.1M
gold.sql 2012-11-21 14:16 1.7K
gold.txt.gz 2012-11-21 14:16 104K
netMm10.sql 2012-11-21 14:16 2.1K
netMm10.txt.gz 2012-11-21 14:16 61M
gap.sql 2012-11-21 14:17 1.6K
gap.txt.gz 2012-11-21 14:17 2.4M
intronEst.sql 2012-11-21 14:18 2.1K
intronEst.txt.gz 2012-11-21 14:18 20K
chainMm10Link.sql 2012-11-21 14:18 1.5K
chainMm10Link.txt.gz 2012-11-21 14:18 428M
cytoBandIdeo.sql 2013-04-28 15:03 1.5K
cytoBandIdeo.txt.gz 2013-04-28 15:03 28K
ucscToINSDC.sql 2013-09-15 12:58 1.4K
ucscToINSDC.txt.gz 2013-09-15 12:58 40K
grp.sql 2014-03-02 03:40 1.3K
grp.txt.gz 2014-03-02 03:40 208
chainHg19.sql 2014-04-06 17:56 1.7K
chainHg19.txt.gz 2014-04-06 17:57 181M
chainHg19Link.sql 2014-04-06 17:57 1.5K
chainHg19Link.txt.gz 2014-04-06 17:58 798M
netHg19.sql 2014-04-06 18:01 2.1K
netHg19.txt.gz 2014-04-06 18:01 64M
cpgIslandExtUnmasked.sql 2014-06-01 13:03 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:03 1.4M
augustusGene.sql 2015-07-26 13:30 1.9K
augustusGene.txt.gz 2015-07-26 13:30 2.2M
microsat.sql 2015-08-23 16:25 1.5K
microsat.txt.gz 2015-08-23 16:25 1.1M
geneid.sql 2015-11-22 15:58 1.9K
geneid.txt.gz 2015-11-22 15:58 2.2M
ensPep.sql 2018-02-04 07:00 1.3K
ensPep.txt.gz 2018-02-04 07:00 6.1M
ensemblSource.sql 2018-02-04 07:00 1.4K
ensemblSource.txt.gz 2018-02-04 07:00 68K
ensGene.sql 2018-02-04 07:02 1.9K
ensGene.txt.gz 2018-02-04 07:02 2.1M
ensGtp.sql 2018-02-04 07:02 1.4K
ensGtp.txt.gz 2018-02-04 07:02 237K
ensemblToGeneName.sql 2018-02-04 07:02 1.4K
ensemblToGeneName.txt.gz 2018-02-04 07:02 122K
chromAlias.sql 2018-02-04 07:02 1.4K
chromAlias.txt.gz 2018-02-04 07:02 50K
ucscToRefSeq.sql 2018-02-18 06:28 1.4K
ucscToRefSeq.txt.gz 2018-02-18 06:28 41K
all_mrna.sql 2020-08-21 17:33 2.1K
all_mrna.txt.gz 2020-08-21 17:33 221K
xenoMrna.sql 2020-08-21 17:33 2.1K
xenoMrna.txt.gz 2020-08-21 17:33 317M
refGene.sql 2020-08-21 17:41 1.9K
refGene.txt.gz 2020-08-21 17:41 38K
refFlat.sql 2020-08-21 17:41 1.7K
refFlat.txt.gz 2020-08-21 17:41 35K
xenoRefGene.sql 2020-08-21 17:41 2.0K
xenoRefGene.txt.gz 2020-08-21 17:41 33M
xenoRefFlat.sql 2020-08-21 17:41 1.7K
xenoRefFlat.txt.gz 2020-08-21 17:41 30M
mrnaOrientInfo.sql 2020-08-21 17:41 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 17:41 49K
refSeqAli.sql 2020-08-21 17:45 2.1K
refSeqAli.txt.gz 2020-08-21 17:45 40K
xenoRefSeqAli.sql 2020-08-21 17:45 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 17:45 34M
gbLoaded.sql 2020-08-21 17:58 1.6K
gbLoaded.txt.gz 2020-08-21 17:58 88K
trackDb.sql 2023-03-28 13:49 2.1K
trackDb.txt.gz 2023-03-28 13:49 26K
hgFindSpec.sql 2023-03-28 13:49 1.8K
hgFindSpec.txt.gz 2023-03-28 13:49 929
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 5.5K
tableList.sql 2024-11-17 03:37 1.6K
tableList.txt.gz 2024-11-17 03:37 2.8K
bigFiles.sql 2024-11-17 03:37 1.4K
bigFiles.txt.gz 2024-11-17 03:37 68