This directory contains a dump of the UCSC genome annotation database for the
Aug. 2012 (allMis0.2/allMis1) assembly of the american alligator genome
(allMis1, International Crocodilian Genomes Working Group) .
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/13409
http://www.ncbi.nlm.nih.gov/genome/assembly/406428
http://www.ncbi.nlm.nih.gov/bioproject/159843
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=allMis1
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/allMis1/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/allMis1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/allMis1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/allMis1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/allMis1/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 allMis1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql allMis1 --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 -
all_est.sql 26-Jun-2016 05:59 2.1K
all_est.txt.gz 26-Jun-2016 05:59 222K
all_mrna.sql 27-Nov-2016 05:13 2.1K
all_mrna.txt.gz 27-Nov-2016 05:13 9.4K
augustusGene.sql 26-Jul-2015 09:51 1.9K
augustusGene.txt.gz 26-Jul-2015 09:51 1.8M
bigFiles.sql 09-Jul-2017 07:23 1.4K
bigFiles.txt.gz 09-Jul-2017 07:23 68
chainHg19.sql 25-Sep-2013 15:23 1.7K
chainHg19.txt.gz 25-Sep-2013 15:23 23M
chainHg19Link.sql 25-Sep-2013 15:24 1.5K
chainHg19Link.txt.gz 25-Sep-2013 15:24 302M
chromInfo.sql 25-Sep-2013 15:25 1.4K
chromInfo.txt.gz 25-Sep-2013 15:25 92K
cpgIslandExt.sql 25-Sep-2013 15:26 1.7K
cpgIslandExt.txt.gz 25-Sep-2013 15:26 530K
cpgIslandExtUnmasked.sql 01-Jun-2014 07:52 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 07:52 781K
cytoBandIdeo.sql 25-Sep-2013 15:26 1.5K
cytoBandIdeo.txt.gz 25-Sep-2013 15:26 86K
estOrientInfo.sql 26-Jun-2016 06:02 1.8K
estOrientInfo.txt.gz 26-Jun-2016 06:02 69K
gap.sql 25-Sep-2013 15:26 1.6K
gap.txt.gz 25-Sep-2013 15:26 1.2M
gbLoaded.sql 09-Jul-2017 07:22 1.6K
gbLoaded.txt.gz 09-Jul-2017 07:22 47K
gc5BaseBw.sql 25-Sep-2013 15:28 1.3K
gc5BaseBw.txt.gz 25-Sep-2013 15:28 63
genscan.sql 25-Sep-2013 15:26 1.7K
genscan.txt.gz 25-Sep-2013 15:26 2.6M
gold.sql 25-Sep-2013 15:26 1.7K
gold.txt.gz 25-Sep-2013 15:26 1.7M
grp.sql 02-Mar-2014 03:37 1.3K
grp.txt.gz 02-Mar-2014 03:37 208
hgFindSpec.sql 09-Jul-2017 07:23 1.7K
hgFindSpec.txt.gz 09-Jul-2017 07:23 502
history.sql 25-Sep-2013 15:26 1.6K
history.txt.gz 25-Sep-2013 15:26 455
intronEst.sql 26-Jun-2016 05:59 2.1K
intronEst.txt.gz 26-Jun-2016 05:59 120K
microsat.sql 23-Aug-2015 09:21 1.5K
microsat.txt.gz 23-Aug-2015 09:21 180K
mrnaOrientInfo.sql 19-Feb-2017 05:37 1.8K
mrnaOrientInfo.txt.gz 19-Feb-2017 05:37 2.7K
nestedRepeats.sql 25-Sep-2013 15:23 1.9K
nestedRepeats.txt.gz 25-Sep-2013 15:23 5.8M
netHg19.sql 25-Sep-2013 15:25 2.1K
netHg19.txt.gz 25-Sep-2013 15:25 15M
refFlat.sql 02-Jul-2017 08:04 1.7K
refFlat.txt.gz 02-Jul-2017 08:04 3.8K
refGene.sql 02-Jul-2017 08:04 1.9K
refGene.txt.gz 02-Jul-2017 08:04 4.2K
refSeqAli.sql 19-Feb-2017 05:46 2.1K
refSeqAli.txt.gz 19-Feb-2017 05:46 4.7K
rmsk.sql 25-Sep-2013 15:28 1.9K
rmsk.txt.gz 25-Sep-2013 15:28 78M
simpleRepeat.sql 25-Sep-2013 15:28 1.9K
simpleRepeat.txt.gz 25-Sep-2013 15:28 9.4M
tableDescriptions.sql 09-Jul-2017 07:22 1.4K
tableDescriptions.txt.gz 09-Jul-2017 07:22 4.1K
tableList.sql 09-Jul-2017 07:22 1.5K
tableList.txt.gz 09-Jul-2017 07:22 2.4K
trackDb.sql 09-Jul-2017 07:23 2.0K
trackDb.txt.gz 09-Jul-2017 07:23 27K
windowmaskerSdust.sql 25-Sep-2013 15:28 1.5K
windowmaskerSdust.txt.gz 25-Sep-2013 15:28 111M
xenoMrna.sql 09-Jul-2017 07:20 2.1K
xenoMrna.txt.gz 09-Jul-2017 07:21 228M
xenoRefFlat.sql 09-Jul-2017 07:22 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 07:22 24M
xenoRefGene.sql 09-Jul-2017 07:23 1.9K
xenoRefGene.txt.gz 09-Jul-2017 07:23 26M
xenoRefSeqAli.sql 09-Jul-2017 07:22 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 07:22 23M