This directory contains a dump of the UCSC genome annotation database for the
Nov. 2017 (Felis_catus_9.0/felCat9) assembly of the cat genome
(felCat9, Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
https://www.ncbi.nlm.nih.gov/genome/78
https://www.ncbi.nlm.nih.gov/genome/assembly/1448961
https://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=felCat9
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.soe.ucsc.edu, then go to
the directory goldenPath/felCat9/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.soe.ucsc.edu/goldenPath/felCat9/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat9/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat9/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat9/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 felCat9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql felCat9 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Cat sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged in
databases.
2. Users are free to use the data in scientific papers analyzing these data
if the providers of these data are properly acknowledged. See
http://genome.ucsc.edu/goldenPath/credits.html for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
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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 -
bigFiles.txt.gz 2024-11-24 03:05 95
bigFiles.sql 2024-11-24 03:05 1.4K
tableList.txt.gz 2024-11-24 03:05 3.8K
tableList.sql 2024-11-24 03:05 1.6K
tableDescriptions.txt.gz 2024-11-23 02:04 6.6K
tableDescriptions.sql 2024-11-23 02:04 1.4K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
trackDb.txt.gz 2024-07-25 09:34 71K
trackDb.sql 2024-07-25 09:34 2.1K
ensPep.txt.gz 2021-05-25 14:34 14M
ensPep.sql 2021-05-25 14:34 1.3K
ensemblSource.txt.gz 2021-05-25 14:34 173K
ensemblSource.sql 2021-05-25 14:34 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:31 250K
ensemblToGeneName.sql 2021-05-25 14:31 1.4K
ensGtp.txt.gz 2021-05-25 14:31 550K
ensGtp.sql 2021-05-25 14:31 1.4K
ensGene.txt.gz 2021-05-25 14:31 3.2M
ensGene.sql 2021-05-25 14:31 1.9K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.6M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 11M
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.0M
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:27 3.7M
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 35K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 379K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
netRBestMm10.txt.gz 2019-06-25 11:00 62M
netRBestMm10.sql 2019-06-25 11:00 2.1K
netRBestHg38.txt.gz 2019-06-25 11:00 66M
netRBestHg38.sql 2019-06-25 11:00 2.1K
chainRBestMm10Link.txt.gz 2019-06-25 10:59 234M
chainRBestMm10Link.sql 2019-06-25 10:58 1.6K
chainRBestMm10.txt.gz 2019-06-25 10:58 869K
chainRBestMm10.sql 2019-06-25 10:58 1.7K
chainRBestHg38Link.txt.gz 2019-06-25 10:57 329M
chainRBestHg38Link.sql 2019-06-25 10:57 1.6K
chainRBestHg38.txt.gz 2019-06-25 10:57 1.3M
chainRBestHg38.sql 2019-06-25 10:57 1.7K
xenoRefSeqAli.txt.gz 2019-05-06 13:15 22M
xenoRefSeqAli.sql 2019-05-06 13:14 2.1K
xenoRefGene.txt.gz 2019-05-06 13:14 25M
xenoRefGene.sql 2019-05-06 13:14 1.9K
xenoRefFlat.txt.gz 2019-05-06 13:14 23M
xenoRefFlat.sql 2019-05-06 13:14 1.7K
xenoMrna.txt.gz 2019-05-06 13:13 225M
xenoMrna.sql 2019-05-06 13:13 2.1K
windowmaskerSdust.txt.gz 2019-05-06 13:13 128M
windowmaskerSdust.sql 2019-05-06 13:12 1.5K
ucscToRefSeq.txt.gz 2019-05-06 13:12 37K
ucscToRefSeq.sql 2019-05-06 13:12 1.4K
ucscToINSDC.txt.gz 2019-05-06 13:12 41K
ucscToINSDC.sql 2019-05-06 13:12 1.4K
tandemDups.txt.gz 2019-05-06 13:12 16M
tandemDups.sql 2019-05-06 13:12 1.8K
simpleRepeat.txt.gz 2019-05-06 13:12 24M
simpleRepeat.sql 2019-05-06 13:12 1.9K
rmsk.txt.gz 2019-05-06 13:12 129M
rmsk.sql 2019-05-06 13:12 1.9K
refSeqAli.txt.gz 2019-05-06 13:12 38K
refSeqAli.sql 2019-05-06 13:12 2.1K
refGene.txt.gz 2019-05-06 13:12 36K
refGene.sql 2019-05-06 13:12 1.9K
refFlat.txt.gz 2019-05-06 13:12 34K
refFlat.sql 2019-05-06 13:12 1.7K
netSynMm10.txt.gz 2019-05-06 13:11 60M
netSynMm10.sql 2019-05-06 13:11 2.1K
netSynHg38.txt.gz 2019-05-06 13:11 62M
netSynHg38.sql 2019-05-06 13:11 2.1K
netMm10.txt.gz 2019-05-06 13:10 62M
netMm10.sql 2019-05-06 13:10 2.1K
netHg38.txt.gz 2019-05-06 13:09 66M
netHg38.sql 2019-05-06 13:09 2.1K
nestedRepeats.txt.gz 2019-05-06 13:09 15M
nestedRepeats.sql 2019-05-06 13:09 1.9K
gap.txt.gz 2019-05-06 13:09 5.9K
gap.sql 2019-05-06 13:09 1.6K
mrnaOrientInfo.txt.gz 2019-05-06 13:09 48K
mrnaOrientInfo.sql 2019-05-06 13:09 1.8K
estOrientInfo.txt.gz 2019-05-06 13:09 16K
estOrientInfo.sql 2019-05-06 13:09 1.8K
microsat.txt.gz 2019-05-06 13:09 1.0M
microsat.sql 2019-05-06 13:09 1.5K
chromInfo.txt.gz 2019-05-06 13:09 25K
chromInfo.sql 2019-05-06 13:09 1.4K
chromAlias.txt.gz 2019-05-06 13:09 52K
chromAlias.sql 2019-05-06 13:09 1.4K
chainSynMm10Link.txt.gz 2019-05-06 13:08 232M
intronEst.txt.gz 2019-05-06 13:08 20K
intronEst.sql 2019-05-06 13:08 2.1K
history.txt.gz 2019-05-06 13:08 934
history.sql 2019-05-06 13:08 1.6K
chainSynMm10Link.sql 2019-05-06 13:08 1.5K
chainSynMm10.txt.gz 2019-05-06 13:08 259K
chainSynMm10.sql 2019-05-06 13:08 1.7K
chainSynHg38Link.txt.gz 2019-05-06 13:06 328M
grp.txt.gz 2019-05-06 13:06 213
grp.sql 2019-05-06 13:06 1.3K
chainSynHg38Link.sql 2019-05-06 13:06 1.5K
chainSynHg38.txt.gz 2019-05-06 13:06 562K
chainSynHg38.sql 2019-05-06 13:06 1.7K
cpgIslandExtUnmasked.txt.gz 2019-05-06 13:06 1.4M
cpgIslandExtUnmasked.sql 2019-05-06 13:06 1.7K
gold.txt.gz 2019-05-06 13:05 65K
gold.sql 2019-05-06 13:05 1.7K
cpgIslandExt.txt.gz 2019-05-06 13:03 1.3M
cpgIslandExt.sql 2019-05-06 13:03 1.7K
genscan.txt.gz 2019-05-06 13:03 3.3M
genscan.sql 2019-05-06 13:03 1.7K
chainMm10Link.txt.gz 2019-05-06 13:01 461M
gc5BaseBw.txt.gz 2019-05-06 13:00 66
gc5BaseBw.sql 2019-05-06 13:00 1.3K
chainMm10Link.sql 2019-05-06 13:00 1.5K
chainMm10.txt.gz 2019-05-06 13:00 59M
chainMm10.sql 2019-05-06 13:00 1.7K
chainHg38Link.txt.gz 2019-05-06 12:55 1.3G
chainHg38Link.sql 2019-05-06 12:54 1.5K
chainHg38.txt.gz 2019-05-06 12:53 376M
cytoBandIdeo.txt.gz 2019-05-06 12:52 24K
cytoBandIdeo.sql 2019-05-06 12:52 1.5K
chainHg38.sql 2019-05-06 12:52 1.7K
augustusGene.txt.gz 2019-05-06 12:52 2.4M
augustusGene.sql 2019-05-06 12:52 1.9K
all_mrna.txt.gz 2019-05-06 12:52 215K
all_mrna.sql 2019-05-06 12:52 2.1K
all_est.txt.gz 2019-05-06 12:52 43K
all_est.sql 2019-05-06 12:52 2.1K