This directory contains a dump of the UCSC genome annotation database for the
Nov. 2014 (Charlie1.0/nasLar1) assembly of the proboscis monkey genome
(nasLar1, Proboscis Monkey Functional Genome Consortium) .
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/7994
http://www.ncbi.nlm.nih.gov/genome/assembly/221311
http://www.ncbi.nlm.nih.gov/bioproject/241312
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=nasLar1
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/nasLar1/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/nasLar1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/nasLar1/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 nasLar1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql nasLar1 --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 -
augustusGene.sql 08-Mar-2017 13:27 1.9K
augustusGene.txt.gz 08-Mar-2017 13:27 1.7M
bigFiles.sql 16-Jul-2017 06:16 1.4K
bigFiles.txt.gz 16-Jul-2017 06:16 69
chainHg38.sql 08-Mar-2017 13:27 1.7K
chainHg38.txt.gz 08-Mar-2017 13:29 197M
chainHg38Link.sql 08-Mar-2017 13:36 1.5K
chainHg38Link.txt.gz 08-Mar-2017 13:43 614M
chainTarSyr2.sql 08-Mar-2017 14:03 1.7K
chainTarSyr2.txt.gz 08-Mar-2017 14:06 232M
chainTarSyr2Link.sql 08-Mar-2017 14:14 1.5K
chainTarSyr2Link.txt.gz 08-Mar-2017 14:25 938M
chromInfo.sql 08-Mar-2017 14:54 1.4K
chromInfo.txt.gz 08-Mar-2017 14:54 1.5M
cpgIslandExt.sql 08-Mar-2017 14:54 1.7K
cpgIslandExt.txt.gz 08-Mar-2017 14:54 490K
cpgIslandExtUnmasked.sql 08-Mar-2017 14:54 1.7K
cpgIslandExtUnmasked.txt.gz 08-Mar-2017 14:54 608K
cytoBandIdeo.sql 08-Mar-2017 14:54 1.5K
cytoBandIdeo.txt.gz 08-Mar-2017 14:54 1.5M
gap.sql 08-Mar-2017 14:54 1.6K
gap.txt.gz 08-Mar-2017 14:54 2.9M
gbLoaded.sql 09-Jul-2017 11:52 1.6K
gbLoaded.txt.gz 09-Jul-2017 11:52 968
gbStatus.sql 16-Jul-2017 06:16 1.9K
gbStatus.txt.gz 16-Jul-2017 06:16 3.4M
gc5BaseBw.sql 08-Mar-2017 14:54 1.3K
gc5BaseBw.txt.gz 08-Mar-2017 14:54 66
genscan.sql 08-Mar-2017 14:54 1.7K
genscan.txt.gz 08-Mar-2017 14:54 2.8M
genscanSubopt.sql 08-Mar-2017 14:59 1.6K
genscanSubopt.txt.gz 08-Mar-2017 14:59 5.2M
gold.sql 08-Mar-2017 15:00 1.7K
gold.txt.gz 08-Mar-2017 15:00 7.7M
grp.sql 08-Mar-2017 15:00 1.3K
grp.txt.gz 08-Mar-2017 15:00 213
hgFindSpec.sql 16-Jul-2017 06:16 1.7K
hgFindSpec.txt.gz 16-Jul-2017 06:16 438
history.sql 08-Mar-2017 14:54 1.6K
history.txt.gz 08-Mar-2017 14:54 520
microsat.sql 08-Mar-2017 13:27 1.5K
microsat.txt.gz 08-Mar-2017 13:27 255K
nestedRepeats.sql 08-Mar-2017 13:36 1.9K
nestedRepeats.txt.gz 08-Mar-2017 13:36 13M
netHg38.sql 08-Mar-2017 15:00 2.1K
netHg38.txt.gz 08-Mar-2017 15:01 28M
netTarSyr2.sql 08-Mar-2017 15:02 2.1K
netTarSyr2.txt.gz 08-Mar-2017 15:04 65M
rmsk.sql 08-Mar-2017 15:05 1.9K
rmsk.txt.gz 08-Mar-2017 15:06 117M
simpleRepeat.sql 08-Mar-2017 14:13 1.9K
simpleRepeat.txt.gz 08-Mar-2017 14:13 18M
tableDescriptions.sql 16-Jul-2017 06:16 1.4K
tableDescriptions.txt.gz 16-Jul-2017 06:16 4.0K
tableList.sql 16-Jul-2017 06:16 1.5K
tableList.txt.gz 16-Jul-2017 06:16 2.2K
trackDb.sql 16-Jul-2017 06:16 2.0K
trackDb.txt.gz 16-Jul-2017 06:16 24K
ucscToINSDC.sql 08-Mar-2017 14:54 1.4K
ucscToINSDC.txt.gz 08-Mar-2017 14:54 2.4M
windowmaskerSdust.sql 08-Mar-2017 14:55 1.5K
windowmaskerSdust.txt.gz 08-Mar-2017 14:56 132M
xenoRefFlat.sql 09-Jul-2017 11:51 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 11:51 20M
xenoRefGene.sql 09-Jul-2017 11:52 1.9K
xenoRefGene.txt.gz 09-Jul-2017 11:52 22M
xenoRefSeqAli.sql 09-Jul-2017 11:52 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 11:52 23M