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 2017-03-08 13:27 1.9K
microsat.sql 2017-03-08 13:27 1.5K
microsat.txt.gz 2017-03-08 13:27 255K
augustusGene.txt.gz 2017-03-08 13:27 1.7M
chainHg38.sql 2017-03-08 13:27 1.7K
chainHg38.txt.gz 2017-03-08 13:29 197M
nestedRepeats.sql 2017-03-08 13:36 1.9K
nestedRepeats.txt.gz 2017-03-08 13:36 13M
chainHg38Link.sql 2017-03-08 13:36 1.5K
chainHg38Link.txt.gz 2017-03-08 13:43 614M
chainTarSyr2.sql 2017-03-08 14:03 1.7K
chainTarSyr2.txt.gz 2017-03-08 14:06 232M
simpleRepeat.sql 2017-03-08 14:13 1.9K
simpleRepeat.txt.gz 2017-03-08 14:13 18M
chainTarSyr2Link.sql 2017-03-08 14:14 1.5K
chainTarSyr2Link.txt.gz 2017-03-08 14:25 938M
chromInfo.sql 2017-03-08 14:54 1.4K
chromInfo.txt.gz 2017-03-08 14:54 1.5M
cpgIslandExt.sql 2017-03-08 14:54 1.7K
cpgIslandExt.txt.gz 2017-03-08 14:54 490K
cpgIslandExtUnmasked.sql 2017-03-08 14:54 1.7K
cpgIslandExtUnmasked.txt.gz 2017-03-08 14:54 608K
history.sql 2017-03-08 14:54 1.6K
history.txt.gz 2017-03-08 14:54 520
ucscToINSDC.sql 2017-03-08 14:54 1.4K
ucscToINSDC.txt.gz 2017-03-08 14:54 2.4M
cytoBandIdeo.sql 2017-03-08 14:54 1.5K
cytoBandIdeo.txt.gz 2017-03-08 14:54 1.5M
gap.sql 2017-03-08 14:54 1.6K
gap.txt.gz 2017-03-08 14:54 2.9M
gc5BaseBw.sql 2017-03-08 14:54 1.3K
gc5BaseBw.txt.gz 2017-03-08 14:54 66
genscan.sql 2017-03-08 14:54 1.7K
genscan.txt.gz 2017-03-08 14:54 2.8M
windowmaskerSdust.sql 2017-03-08 14:55 1.5K
windowmaskerSdust.txt.gz 2017-03-08 14:56 132M
genscanSubopt.sql 2017-03-08 14:59 1.6K
genscanSubopt.txt.gz 2017-03-08 14:59 5.2M
gold.sql 2017-03-08 15:00 1.7K
gold.txt.gz 2017-03-08 15:00 7.7M
grp.sql 2017-03-08 15:00 1.3K
grp.txt.gz 2017-03-08 15:00 213
netHg38.sql 2017-03-08 15:00 2.1K
netHg38.txt.gz 2017-03-08 15:01 28M
netTarSyr2.sql 2017-03-08 15:02 2.1K
netTarSyr2.txt.gz 2017-03-08 15:04 65M
rmsk.sql 2017-03-08 15:05 1.9K
rmsk.txt.gz 2017-03-08 15:06 117M
gbStatus.sql 2017-12-31 08:48 1.9K
gbStatus.txt.gz 2017-12-31 08:48 3.4M
xenoRefGene.sql 2020-08-19 20:16 2.0K
xenoRefGene.txt.gz 2020-08-19 20:16 30M
xenoRefFlat.sql 2020-08-19 20:16 1.7K
xenoRefFlat.txt.gz 2020-08-19 20:16 27M
xenoRefSeqAli.sql 2020-08-19 20:16 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 20:16 31M
gbLoaded.sql 2020-08-19 20:19 1.6K
gbLoaded.txt.gz 2020-08-19 20:19 5.7K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 34K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 569
tableDescriptions.sql 2024-12-07 02:03 1.5K
tableDescriptions.txt.gz 2024-12-07 02:03 5.1K
tableList.sql 2024-12-08 03:16 1.6K
tableList.txt.gz 2024-12-08 03:16 2.1K
bigFiles.sql 2024-12-08 03:16 1.4K
bigFiles.txt.gz 2024-12-08 03:16 69