This directory contains a dump of the UCSC genome annotation database for
the Aug. 2011 (LatCha1/latCha1) assembly of the coelacanth genome (latCha1,
Broad LatCha1 (GCA_000225785.1)). 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/3262
http://www.ncbi.nlm.nih.gov/genome/assembly/303548
http://www.ncbi.nlm.nih.gov/bioproject/56111
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=latCha1
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/latCha1/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/latCha1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/latCha1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/latCha1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/latCha1/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 latCha1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql latCha1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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The Coelacanth sequence is made freely available before scientific publication
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 particular
genes and regions if the provider of these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves 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. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
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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 -
chainMm10Link.sql 2012-11-06 14:12 1.5K
chainMm10Link.txt.gz 2012-11-06 14:12 140M
gc5BaseBw.sql 2012-11-06 14:15 1.3K
gc5BaseBw.txt.gz 2012-11-06 14:15 63
gold.sql 2012-11-06 14:15 1.7K
gold.txt.gz 2012-11-06 14:15 4.5M
chainFr3.sql 2012-11-06 14:16 1.7K
chainFr3.txt.gz 2012-11-06 14:16 9.7M
gap.sql 2012-11-06 14:16 1.6K
gap.txt.gz 2012-11-06 14:16 3.4M
chainMm10.sql 2012-11-06 14:16 1.7K
chainMm10.txt.gz 2012-11-06 14:16 16M
netMm10.sql 2012-11-06 14:16 2.1K
netMm10.txt.gz 2012-11-06 14:16 7.7M
rmsk.sql 2012-11-06 14:16 1.9K
rmsk.txt.gz 2012-11-06 14:16 42M
netFr3.sql 2012-11-06 14:16 2.1K
netFr3.txt.gz 2012-11-06 14:16 6.6M
nestedRepeats.sql 2012-11-06 14:16 1.9K
nestedRepeats.txt.gz 2012-11-06 14:16 3.4M
simpleRepeat.sql 2012-11-06 14:16 1.9K
simpleRepeat.txt.gz 2012-11-06 14:16 14M
cpgIslandExt.sql 2012-11-06 14:17 1.7K
cpgIslandExt.txt.gz 2012-11-06 14:17 182K
windowmaskerSdust.sql 2012-11-06 14:17 1.5K
windowmaskerSdust.txt.gz 2012-11-06 14:17 132M
chromInfo.sql 2012-11-06 14:17 1.4K
chromInfo.txt.gz 2012-11-06 14:17 113K
genscan.sql 2012-11-06 14:17 1.7K
genscan.txt.gz 2012-11-06 14:17 1.8M
history.sql 2012-11-06 14:17 1.6K
history.txt.gz 2012-11-06 14:17 596
chainFr3Link.sql 2012-11-06 14:19 1.5K
chainFr3Link.txt.gz 2012-11-06 14:19 41M
cytoBandIdeo.sql 2013-04-28 18:02 1.5K
cytoBandIdeo.txt.gz 2013-04-28 18:02 115K
ucscToINSDC.sql 2013-09-15 15:42 1.4K
ucscToINSDC.txt.gz 2013-09-15 15:42 167K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 16:01 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 16:01 872K
augustusGene.sql 2015-07-26 15:56 1.9K
augustusGene.txt.gz 2015-07-26 15:56 1.8M
microsat.sql 2015-08-23 20:34 1.5K
microsat.txt.gz 2015-08-23 20:34 663K
mrnaOrientInfo.sql 2016-05-15 10:21 1.8K
mrnaOrientInfo.txt.gz 2016-05-15 10:21 1.3K
all_mrna.sql 2016-05-15 10:23 2.1K
all_mrna.txt.gz 2016-05-15 10:23 5.1K
chromAlias.sql 2018-02-18 07:15 1.4K
chromAlias.txt.gz 2018-02-18 07:15 215K
ucscToRefSeq.sql 2018-02-18 07:15 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:15 169K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 91
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:27 2.6M
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 796
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.2M
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 235K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 7.8M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.6M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.1M
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 615K
xenoMrna.sql 2020-08-19 13:07 2.1K
xenoMrna.txt.gz 2020-08-19 13:07 227M
xenoRefGene.sql 2020-08-19 13:31 2.0K
xenoRefGene.txt.gz 2020-08-19 13:31 29M
xenoRefFlat.sql 2020-08-19 13:31 1.7K
xenoRefFlat.txt.gz 2020-08-19 13:31 27M
xenoRefSeqAli.sql 2020-08-19 13:31 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 13:31 26M
gbLoaded.sql 2020-08-19 13:31 1.6K
gbLoaded.txt.gz 2020-08-19 13:31 15K
ensGene.sql 2021-05-25 14:34 1.9K
ensGene.txt.gz 2021-05-25 14:34 2.1M
ensGtp.sql 2021-05-25 14:34 1.4K
ensGtp.txt.gz 2021-05-25 14:34 255K
ensemblToGeneName.sql 2021-05-25 14:34 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:34 131K
ensemblSource.sql 2021-05-25 14:36 1.4K
ensemblSource.txt.gz 2021-05-25 14:36 71K
ensPep.sql 2021-05-25 14:36 1.3K
ensPep.txt.gz 2021-05-25 14:36 6.4M
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 29K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
tableList.sql 2024-11-17 03:36 1.6K
tableList.txt.gz 2024-11-17 03:36 2.9K
bigFiles.sql 2024-11-17 03:36 1.4K
bigFiles.txt.gz 2024-11-17 03:36 94