This directory contains a dump of the UCSC genome annotation database for the
Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1) assembly of the elephant shark genome
(calMil1, Institute of Molecular and Cell Biology, Singapore) .
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/689
http://www.ncbi.nlm.nih.gov/genome/assembly/85971
http://www.ncbi.nlm.nih.gov/bioproject/18361
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=calMil1
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/calMil1/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/calMil1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calMil1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calMil1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calMil1/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 calMil1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calMil1 --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.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2014-05-08 14:04 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
extNcbiRefSeq.txt.gz 2020-05-10 03:26 90
bigFiles.txt.gz 2024-04-14 03:36 95
grp.txt.gz 2014-08-03 06:48 200
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 325
history.txt.gz 2014-05-08 14:03 402
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:52 1.2K
gc5BaseBw.sql 2014-05-08 14:04 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ensPep.sql 2021-05-25 14:24 1.3K
grp.sql 2014-08-03 06:48 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ensemblSource.sql 2021-05-25 14:24 1.4K
chromInfo.sql 2014-05-08 14:03 1.4K
bigFiles.sql 2024-04-14 03:36 1.4K
ensemblToGeneName.sql 2021-05-25 14:22 1.4K
chromAlias.sql 2020-04-12 03:25 1.4K
ucscToINSDC.sql 2014-05-08 14:04 1.4K
ucscToRefSeq.sql 2018-02-18 05:32 1.4K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
ensGtp.sql 2021-05-25 14:22 1.4K
tableDescriptions.sql 2024-04-13 02:03 1.5K
microsat.sql 2015-08-23 11:24 1.5K
windowmaskerSdust.sql 2014-05-08 14:04 1.5K
cytoBandIdeo.sql 2014-05-08 14:03 1.5K
chainRn6Link.sql 2017-03-26 15:21 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
genscanSubopt.sql 2014-05-08 14:03 1.6K
history.sql 2014-05-08 14:03 1.6K
tableList.sql 2024-04-14 03:36 1.6K
gap.sql 2014-05-08 14:03 1.6K
gbLoaded.sql 2020-08-18 11:45 1.6K
gold.sql 2014-05-08 14:03 1.7K
genscan.sql 2014-05-08 14:03 1.7K
cpgIslandExt.sql 2014-05-08 14:03 1.7K
chainRn6.sql 2017-03-26 15:18 1.7K
cpgIslandExtUnmasked.sql 2014-05-08 14:03 1.7K
xenoRefFlat.sql 2020-08-18 11:40 1.7K
hgFindSpec.sql 2023-12-05 13:52 1.8K
estOrientInfo.sql 2016-05-15 07:51 1.8K
mrnaOrientInfo.sql 2017-04-09 11:47 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:52 1.8K
rmsk.sql 2014-05-08 14:04 1.9K
simpleRepeat.sql 2014-05-08 14:04 1.9K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
nestedRepeats.sql 2014-05-08 14:03 1.9K
augustusGene.sql 2015-07-26 10:55 1.9K
ensGene.sql 2021-05-25 14:22 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
xenoRefGene.sql 2020-08-18 11:37 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
trackDb.sql 2023-12-05 13:52 2.1K
netRn6.sql 2017-03-26 15:43 2.1K
trackDb_pushedout.sql 2023-12-05 13:52 2.1K
all_est.sql 2016-05-15 07:51 2.1K
all_mrna.sql 2017-04-09 11:50 2.1K
intronEst.sql 2016-05-15 07:51 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
xenoRefSeqAli.sql 2020-08-18 11:45 2.1K
tableList.txt.gz 2024-04-14 03:36 3.1K
tableDescriptions.txt.gz 2024-04-13 02:03 6.3K
trackDb.txt.gz 2023-12-05 13:52 31K
trackDb_pushedout.txt.gz 2023-12-05 13:52 31K
microsat.txt.gz 2015-08-23 11:24 33K
gbLoaded.txt.gz 2020-08-18 11:45 44K
cytoBandIdeo.txt.gz 2014-05-08 14:03 71K
chromInfo.txt.gz 2014-05-08 14:03 74K
ucscToINSDC.txt.gz 2014-05-08 14:04 122K
ensemblSource.txt.gz 2021-05-25 14:24 124K
ucscToRefSeq.txt.gz 2018-02-18 05:32 125K
ensemblToGeneName.txt.gz 2021-05-25 14:22 167K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 185K
chromAlias.txt.gz 2020-04-12 03:25 206K
cpgIslandExt.txt.gz 2014-05-08 14:03 376K
ensGtp.txt.gz 2021-05-25 14:22 412K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 458K
mrnaOrientInfo.txt.gz 2017-04-09 11:47 485K
gap.txt.gz 2014-05-08 14:03 571K
cpgIslandExtUnmasked.txt.gz 2014-05-08 14:03 710K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 895K
gold.txt.gz 2014-05-08 14:03 898K
estOrientInfo.txt.gz 2016-05-15 07:51 1.2M
augustusGene.txt.gz 2015-07-26 10:55 1.7M
genscan.txt.gz 2014-05-08 14:03 1.9M
nestedRepeats.txt.gz 2014-05-08 14:03 2.0M
intronEst.txt.gz 2016-05-15 07:51 2.0M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.1M
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.1M
all_mrna.txt.gz 2017-04-09 11:50 2.2M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 2.5M
ensGene.txt.gz 2021-05-25 14:22 2.8M
genscanSubopt.txt.gz 2014-05-08 14:03 2.8M
all_est.txt.gz 2016-05-15 07:51 3.9M
netRn6.txt.gz 2017-03-26 15:43 5.6M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 6.0M
ensPep.txt.gz 2021-05-25 14:24 7.0M
simpleRepeat.txt.gz 2014-05-08 14:04 8.6M
xenoRefSeqAli.txt.gz 2020-08-18 11:45 24M
xenoRefFlat.txt.gz 2020-08-18 11:40 24M
xenoRefGene.txt.gz 2020-08-18 11:37 27M
rmsk.txt.gz 2014-05-08 14:04 36M
windowmaskerSdust.txt.gz 2014-05-08 14:04 50M
chainRn6.txt.gz 2017-03-26 15:19 78M
chainRn6Link.txt.gz 2017-03-26 15:24 312M