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 -
chainHg38Link.txt.gz 2019-05-06 12:55 1.3G
chainMm10Link.txt.gz 2019-05-06 13:01 461M
chainHg38.txt.gz 2019-05-06 12:53 376M
chainRBestHg38Link.txt.gz 2019-06-25 10:57 329M
chainSynHg38Link.txt.gz 2019-05-06 13:06 328M
chainRBestMm10Link.txt.gz 2019-06-25 10:59 234M
chainSynMm10Link.txt.gz 2019-05-06 13:08 232M
xenoMrna.txt.gz 2019-05-06 13:13 225M
rmsk.txt.gz 2019-05-06 13:12 129M
windowmaskerSdust.txt.gz 2019-05-06 13:13 128M
netHg38.txt.gz 2019-05-06 13:09 66M
netRBestHg38.txt.gz 2019-06-25 11:00 66M
netMm10.txt.gz 2019-05-06 13:10 62M
netSynHg38.txt.gz 2019-05-06 13:11 62M
netRBestMm10.txt.gz 2019-06-25 11:00 62M
netSynMm10.txt.gz 2019-05-06 13:11 60M
chainMm10.txt.gz 2019-05-06 13:00 59M
xenoRefGene.txt.gz 2019-05-06 13:14 25M
simpleRepeat.txt.gz 2019-05-06 13:12 24M
xenoRefFlat.txt.gz 2019-05-06 13:14 23M
xenoRefSeqAli.txt.gz 2019-05-06 13:15 22M
tandemDups.txt.gz 2019-05-06 13:12 16M
nestedRepeats.txt.gz 2019-05-06 13:09 15M
ensPep.txt.gz 2021-05-25 14:34 14M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 11M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.0M
ncbiRefSeq.txt.gz 2020-05-10 03:27 3.7M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.6M
genscan.txt.gz 2019-05-06 13:03 3.3M
ensGene.txt.gz 2021-05-25 14:31 3.2M
augustusGene.txt.gz 2019-05-06 12:52 2.4M
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.9M
cpgIslandExtUnmasked.txt.gz 2019-05-06 13:06 1.4M
chainRBestHg38.txt.gz 2019-06-25 10:57 1.3M
cpgIslandExt.txt.gz 2019-05-06 13:03 1.3M
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 1.1M
microsat.txt.gz 2019-05-06 13:09 1.0M
chainRBestMm10.txt.gz 2019-06-25 10:58 869K
chainSynHg38.txt.gz 2019-05-06 13:06 562K
ensGtp.txt.gz 2021-05-25 14:31 550K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 379K
chainSynMm10.txt.gz 2019-05-06 13:08 259K
ensemblToGeneName.txt.gz 2021-05-25 14:31 250K
all_mrna.txt.gz 2019-05-06 12:52 215K
ensemblSource.txt.gz 2021-05-25 14:34 173K
gold.txt.gz 2019-05-06 13:05 65K
trackDb.txt.gz 2024-01-31 15:13 55K
chromAlias.txt.gz 2019-05-06 13:09 52K
mrnaOrientInfo.txt.gz 2019-05-06 13:09 48K
all_est.txt.gz 2019-05-06 12:52 43K
ucscToINSDC.txt.gz 2019-05-06 13:12 41K
refSeqAli.txt.gz 2019-05-06 13:12 38K
ucscToRefSeq.txt.gz 2019-05-06 13:12 37K
refGene.txt.gz 2019-05-06 13:12 36K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 35K
refFlat.txt.gz 2019-05-06 13:12 34K
trackDb_pushedout.txt.gz 2023-12-05 13:50 33K
chromInfo.txt.gz 2019-05-06 13:09 25K
cytoBandIdeo.txt.gz 2019-05-06 12:52 24K
intronEst.txt.gz 2019-05-06 13:08 20K
estOrientInfo.txt.gz 2019-05-06 13:09 16K
tableDescriptions.txt.gz 2024-04-20 02:04 6.6K
gap.txt.gz 2019-05-06 13:09 5.9K
tableList.txt.gz 2024-04-21 03:06 4.0K
xenoRefSeqAli.sql 2019-05-06 13:14 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
refSeqAli.sql 2019-05-06 13:12 2.1K
intronEst.sql 2019-05-06 13:08 2.1K
xenoMrna.sql 2019-05-06 13:13 2.1K
all_mrna.sql 2019-05-06 12:52 2.1K
netRBestMm10.sql 2019-06-25 11:00 2.1K
netRBestHg38.sql 2019-06-25 11:00 2.1K
all_est.sql 2019-05-06 12:52 2.1K
netSynMm10.sql 2019-05-06 13:11 2.1K
netSynHg38.sql 2019-05-06 13:11 2.1K
netMm10.sql 2019-05-06 13:10 2.1K
netHg38.sql 2019-05-06 13:09 2.1K
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb.sql 2024-01-31 15:13 2.1K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ensGene.sql 2021-05-25 14:31 1.9K
augustusGene.sql 2019-05-06 12:52 1.9K
xenoRefGene.sql 2019-05-06 13:14 1.9K
nestedRepeats.sql 2019-05-06 13:09 1.9K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
simpleRepeat.sql 2019-05-06 13:12 1.9K
refGene.sql 2019-05-06 13:12 1.9K
rmsk.sql 2019-05-06 13:12 1.9K
tandemDups.sql 2019-05-06 13:12 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
mrnaOrientInfo.sql 2019-05-06 13:09 1.8K
estOrientInfo.sql 2019-05-06 13:09 1.8K
hgFindSpec.sql 2024-01-31 15:13 1.8K
xenoRefFlat.sql 2019-05-06 13:14 1.7K
chainRBestMm10.sql 2019-06-25 10:58 1.7K
chainRBestHg38.sql 2019-06-25 10:57 1.7K
cpgIslandExtUnmasked.sql 2019-05-06 13:06 1.7K
chainSynMm10.sql 2019-05-06 13:08 1.7K
chainSynHg38.sql 2019-05-06 13:06 1.7K
refFlat.sql 2019-05-06 13:12 1.7K
chainMm10.sql 2019-05-06 13:00 1.7K
chainHg38.sql 2019-05-06 12:52 1.7K
cpgIslandExt.sql 2019-05-06 13:03 1.7K
genscan.sql 2019-05-06 13:03 1.7K
gold.sql 2019-05-06 13:05 1.7K
gap.sql 2019-05-06 13:09 1.6K
tableList.sql 2024-04-21 03:06 1.6K
history.sql 2019-05-06 13:08 1.6K
chainRBestMm10Link.sql 2019-06-25 10:58 1.6K
chainRBestHg38Link.sql 2019-06-25 10:57 1.6K
chainSynMm10Link.sql 2019-05-06 13:08 1.5K
chainSynHg38Link.sql 2019-05-06 13:06 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
chainMm10Link.sql 2019-05-06 13:00 1.5K
chainHg38Link.sql 2019-05-06 12:54 1.5K
cytoBandIdeo.sql 2019-05-06 12:52 1.5K
windowmaskerSdust.sql 2019-05-06 13:12 1.5K
microsat.sql 2019-05-06 13:09 1.5K
tableDescriptions.sql 2024-04-20 02:04 1.5K
ensGtp.sql 2021-05-25 14:31 1.4K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
ucscToRefSeq.sql 2019-05-06 13:12 1.4K
ucscToINSDC.sql 2019-05-06 13:12 1.4K
chromAlias.sql 2019-05-06 13:09 1.4K
ensemblToGeneName.sql 2021-05-25 14:31 1.4K
bigFiles.sql 2024-04-21 03:06 1.4K
chromInfo.sql 2019-05-06 13:09 1.4K
ensemblSource.sql 2021-05-25 14:34 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
grp.sql 2019-05-06 13:06 1.3K
ensPep.sql 2021-05-25 14:34 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.3K
gc5BaseBw.sql 2019-05-06 13:00 1.3K
hgFindSpec.txt.gz 2024-01-31 15:13 1.3K
history.txt.gz 2019-05-06 13:08 934
grp.txt.gz 2019-05-06 13:06 213
bigFiles.txt.gz 2024-04-21 03:06 95
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
gc5BaseBw.txt.gz 2019-05-06 13:00 66