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 -
nestedRepeats.sql 2014-05-08 14:03 1.9K
nestedRepeats.txt.gz 2014-05-08 14:03 2.0M
chromInfo.sql 2014-05-08 14:03 1.4K
chromInfo.txt.gz 2014-05-08 14:03 74K
cpgIslandExt.sql 2014-05-08 14:03 1.7K
cpgIslandExt.txt.gz 2014-05-08 14:03 376K
cpgIslandExtUnmasked.sql 2014-05-08 14:03 1.7K
cpgIslandExtUnmasked.txt.gz 2014-05-08 14:03 710K
genscan.sql 2014-05-08 14:03 1.7K
genscan.txt.gz 2014-05-08 14:03 1.9M
cytoBandIdeo.sql 2014-05-08 14:03 1.5K
cytoBandIdeo.txt.gz 2014-05-08 14:03 71K
genscanSubopt.sql 2014-05-08 14:03 1.6K
genscanSubopt.txt.gz 2014-05-08 14:03 2.8M
gap.sql 2014-05-08 14:03 1.6K
gold.sql 2014-05-08 14:03 1.7K
gold.txt.gz 2014-05-08 14:03 898K
gap.txt.gz 2014-05-08 14:03 571K
history.sql 2014-05-08 14:03 1.6K
history.txt.gz 2014-05-08 14:03 402
gc5BaseBw.sql 2014-05-08 14:04 1.3K
gc5BaseBw.txt.gz 2014-05-08 14:04 66
rmsk.sql 2014-05-08 14:04 1.9K
rmsk.txt.gz 2014-05-08 14:04 36M
simpleRepeat.sql 2014-05-08 14:04 1.9K
simpleRepeat.txt.gz 2014-05-08 14:04 8.6M
ucscToINSDC.sql 2014-05-08 14:04 1.4K
ucscToINSDC.txt.gz 2014-05-08 14:04 122K
windowmaskerSdust.sql 2014-05-08 14:04 1.5K
windowmaskerSdust.txt.gz 2014-05-08 14:04 50M
grp.sql 2014-08-03 06:48 1.3K
grp.txt.gz 2014-08-03 06:48 200
augustusGene.sql 2015-07-26 10:55 1.9K
augustusGene.txt.gz 2015-07-26 10:55 1.7M
microsat.sql 2015-08-23 11:24 1.5K
microsat.txt.gz 2015-08-23 11:24 33K
all_est.sql 2016-05-15 07:51 2.1K
intronEst.sql 2016-05-15 07:51 2.1K
intronEst.txt.gz 2016-05-15 07:51 2.0M
all_est.txt.gz 2016-05-15 07:51 3.9M
estOrientInfo.sql 2016-05-15 07:51 1.8K
estOrientInfo.txt.gz 2016-05-15 07:51 1.2M
chainRn6.sql 2017-03-26 15:18 1.7K
chainRn6.txt.gz 2017-03-26 15:19 78M
chainRn6Link.sql 2017-03-26 15:21 1.5K
chainRn6Link.txt.gz 2017-03-26 15:24 312M
netRn6.sql 2017-03-26 15:43 2.1K
netRn6.txt.gz 2017-03-26 15:43 5.6M
mrnaOrientInfo.sql 2017-04-09 11:47 1.8K
mrnaOrientInfo.txt.gz 2017-04-09 11:47 485K
all_mrna.sql 2017-04-09 11:50 2.1K
all_mrna.txt.gz 2017-04-09 11:50 2.2M
ucscToRefSeq.sql 2018-02-18 05:32 1.4K
ucscToRefSeq.txt.gz 2018-02-18 05:32 125K
chromAlias.sql 2020-04-12 03:25 1.4K
chromAlias.txt.gz 2020-04-12 03:25 206K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:26 90
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 325
ncbiRefSeq.txt.gz 2020-05-10 03:26 2.1M
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 185K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 895K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 6.0M
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 2.1M
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 2.5M
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 458K
xenoRefGene.sql 2020-08-18 11:37 2.0K
xenoRefGene.txt.gz 2020-08-18 11:37 27M
xenoRefFlat.sql 2020-08-18 11:40 1.7K
xenoRefFlat.txt.gz 2020-08-18 11:40 24M
xenoRefSeqAli.sql 2020-08-18 11:45 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 11:45 24M
gbLoaded.sql 2020-08-18 11:45 1.6K
gbLoaded.txt.gz 2020-08-18 11:45 44K
ensGene.sql 2021-05-25 14:22 1.9K
ensGene.txt.gz 2021-05-25 14:22 2.8M
ensGtp.sql 2021-05-25 14:22 1.4K
ensGtp.txt.gz 2021-05-25 14:22 412K
ensemblToGeneName.sql 2021-05-25 14:22 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:22 167K
ensemblSource.sql 2021-05-25 14:24 1.4K
ensemblSource.txt.gz 2021-05-25 14:24 124K
ensPep.sql 2021-05-25 14:24 1.3K
ensPep.txt.gz 2021-05-25 14:24 7.0M
trackDb.sql 2023-12-05 13:52 2.1K
trackDb.txt.gz 2023-12-05 13:52 31K
hgFindSpec.sql 2023-12-05 13:52 1.8K
hgFindSpec.txt.gz 2023-12-05 13:52 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 03:38 1.6K
tableList.txt.gz 2024-11-17 03:38 2.9K
bigFiles.sql 2024-11-17 03:38 1.4K
bigFiles.txt.gz 2024-11-17 03:38 95