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 -
gc5BaseBw.txt.gz 2012-11-21 14:13 63
bigFiles.txt.gz 2024-04-21 03:37 68
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2012-11-21 14:16 514
hgFindSpec_pushedout.txt.gz 2021-12-27 12:20 885
hgFindSpec.txt.gz 2023-03-28 13:49 929
gc5BaseBw.sql 2012-11-21 14:13 1.3K
ensPep.sql 2018-02-04 07:00 1.3K
grp.sql 2014-03-02 03:40 1.3K
ensemblSource.sql 2018-02-04 07:00 1.4K
chromInfo.sql 2012-11-21 14:16 1.4K
ensemblToGeneName.sql 2018-02-04 07:02 1.4K
bigFiles.sql 2024-04-21 03:37 1.4K
ensGtp.sql 2018-02-04 07:02 1.4K
chromAlias.sql 2018-02-04 07:02 1.4K
ucscToINSDC.sql 2013-09-15 12:58 1.4K
ucscToRefSeq.sql 2018-02-18 06:28 1.4K
tableDescriptions.sql 2024-04-20 02:03 1.5K
microsat.sql 2015-08-23 16:25 1.5K
windowmaskerSdust.sql 2012-11-21 14:12 1.5K
cytoBandIdeo.sql 2013-04-28 15:03 1.5K
chainHg19Link.sql 2014-04-06 17:57 1.5K
chainMm10Link.sql 2012-11-21 14:18 1.5K
history.sql 2012-11-21 14:16 1.6K
tableList.sql 2024-04-21 03:37 1.6K
gap.sql 2012-11-21 14:17 1.6K
gbLoaded.sql 2020-08-21 17:58 1.6K
gold.sql 2012-11-21 14:16 1.7K
genscan.sql 2012-11-21 14:16 1.7K
cpgIslandExt.sql 2012-11-21 14:11 1.7K
chainHg19.sql 2014-04-06 17:56 1.7K
chainMm10.sql 2012-11-21 14:10 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 13:03 1.7K
refFlat.sql 2020-08-21 17:41 1.7K
xenoRefFlat.sql 2020-08-21 17:41 1.7K
hgFindSpec.sql 2023-03-28 13:49 1.8K
estOrientInfo.sql 2012-11-21 14:12 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:20 1.8K
mrnaOrientInfo.sql 2020-08-21 17:41 1.8K
rmsk.sql 2012-11-21 14:12 1.9K
geneid.sql 2015-11-22 15:58 1.9K
ensGene.sql 2018-02-04 07:02 1.9K
simpleRepeat.sql 2012-11-21 14:10 1.9K
nestedRepeats.sql 2012-11-21 14:13 1.9K
augustusGene.sql 2015-07-26 13:30 1.9K
refGene.sql 2020-08-21 17:41 1.9K
xenoRefGene.sql 2020-08-21 17:41 2.0K
trackDb.sql 2023-03-28 13:49 2.1K
trackDb_pushedout.sql 2021-12-27 12:20 2.1K
netHg19.sql 2014-04-06 18:01 2.1K
netMm10.sql 2012-11-21 14:16 2.1K
all_est.sql 2012-11-21 14:11 2.1K
intronEst.sql 2012-11-21 14:18 2.1K
all_mrna.sql 2020-08-21 17:33 2.1K
xenoMrna.sql 2020-08-21 17:33 2.1K
refSeqAli.sql 2020-08-21 17:45 2.1K
xenoRefSeqAli.sql 2020-08-21 17:45 2.1K
tableList.txt.gz 2024-04-21 03:37 3.0K
tableDescriptions.txt.gz 2024-04-20 02:03 5.5K
estOrientInfo.txt.gz 2012-11-21 14:12 14K
intronEst.txt.gz 2012-11-21 14:18 20K
trackDb_pushedout.txt.gz 2021-12-27 12:20 26K
trackDb.txt.gz 2023-03-28 13:49 26K
cytoBandIdeo.txt.gz 2013-04-28 15:03 28K
chromInfo.txt.gz 2012-11-21 14:16 29K
refFlat.txt.gz 2020-08-21 17:41 35K
refGene.txt.gz 2020-08-21 17:41 38K
all_est.txt.gz 2012-11-21 14:11 40K
ucscToINSDC.txt.gz 2013-09-15 12:58 40K
refSeqAli.txt.gz 2020-08-21 17:45 40K
ucscToRefSeq.txt.gz 2018-02-18 06:28 41K
mrnaOrientInfo.txt.gz 2020-08-21 17:41 49K
chromAlias.txt.gz 2018-02-04 07:02 50K
ensemblSource.txt.gz 2018-02-04 07:00 68K
gbLoaded.txt.gz 2020-08-21 17:58 88K
gold.txt.gz 2012-11-21 14:16 104K
ensemblToGeneName.txt.gz 2018-02-04 07:02 122K
all_mrna.txt.gz 2020-08-21 17:33 221K
ensGtp.txt.gz 2018-02-04 07:02 237K
microsat.txt.gz 2015-08-23 16:25 1.1M
cpgIslandExt.txt.gz 2012-11-21 14:11 1.2M
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:03 1.4M
ensGene.txt.gz 2018-02-04 07:02 2.1M
geneid.txt.gz 2015-11-22 15:58 2.2M
augustusGene.txt.gz 2015-07-26 13:30 2.2M
gap.txt.gz 2012-11-21 14:17 2.4M
genscan.txt.gz 2012-11-21 14:16 3.1M
ensPep.txt.gz 2018-02-04 07:00 6.1M
nestedRepeats.txt.gz 2012-11-21 14:13 14M
simpleRepeat.txt.gz 2012-11-21 14:10 19M
xenoRefFlat.txt.gz 2020-08-21 17:41 30M
xenoRefGene.txt.gz 2020-08-21 17:41 33M
xenoRefSeqAli.txt.gz 2020-08-21 17:45 34M
chainMm10.txt.gz 2012-11-21 14:10 50M
netMm10.txt.gz 2012-11-21 14:16 61M
netHg19.txt.gz 2014-04-06 18:01 64M
rmsk.txt.gz 2012-11-21 14:12 120M
windowmaskerSdust.txt.gz 2012-11-21 14:13 125M
chainHg19.txt.gz 2014-04-06 17:57 181M
xenoMrna.txt.gz 2020-08-21 17:33 317M
chainMm10Link.txt.gz 2012-11-21 14:18 428M
chainHg19Link.txt.gz 2014-04-06 17:58 798M