This directory contains a dump of the UCSC genome annotation database for the
Jun. 2015 (MPI-EVA AptMant0/aptMan1) assembly of the brown kiwi genome
(aptMan1, Max-Plank Institute for Evolutionary Anthropology AptMant0) .
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/10907
http://www.ncbi.nlm.nih.gov/assembly/GCF_001039765.1
http://www.ncbi.nlm.nih.gov/bioproject/287231
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=aptMan1
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/aptMan1/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/aptMan1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/aptMan1/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 aptMan1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql aptMan1 --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 2016-03-18 11:11 1.9K
augustusGene.txt.gz 2016-03-18 11:11 1.5M
gc5BaseBw.sql 2016-03-18 11:11 1.3K
gc5BaseBw.txt.gz 2016-03-18 11:11 66
microsat.sql 2016-03-18 11:11 1.5K
microsat.txt.gz 2016-03-18 11:11 47K
chromInfo.sql 2016-03-18 11:11 1.4K
chromInfo.txt.gz 2016-03-18 11:11 124K
gold.sql 2016-03-18 11:11 1.7K
gold.txt.gz 2016-03-18 11:11 3.3M
cpgIslandExt.sql 2016-03-18 11:11 1.7K
cpgIslandExt.txt.gz 2016-03-18 11:11 1.1M
cpgIslandExtUnmasked.sql 2016-03-18 11:11 1.7K
cpgIslandExtUnmasked.txt.gz 2016-03-18 11:11 1.2M
cytoBandIdeo.sql 2016-03-18 11:11 1.5K
cytoBandIdeo.txt.gz 2016-03-18 11:11 121K
grp.sql 2016-03-18 11:11 1.3K
grp.txt.gz 2016-03-18 11:11 213
gap.sql 2016-03-18 11:11 1.6K
gap.txt.gz 2016-03-18 11:11 2.4M
history.sql 2016-03-18 11:11 1.6K
history.txt.gz 2016-03-18 11:11 377
refSeqAli.sql 2016-03-18 11:11 2.1K
refSeqAli.txt.gz 2016-03-18 11:11 161
rmsk.sql 2016-03-18 11:11 1.9K
rmsk.txt.gz 2016-03-18 11:11 12M
genscan.sql 2016-03-18 11:11 1.7K
genscan.txt.gz 2016-03-18 11:11 1.9M
genscanSubopt.sql 2016-03-18 11:11 1.6K
genscanSubopt.txt.gz 2016-03-18 11:11 4.8M
simpleRepeat.sql 2016-03-18 11:11 1.9K
simpleRepeat.txt.gz 2016-03-18 11:11 24M
windowmaskerSdust.sql 2016-03-18 11:11 1.5K
windowmaskerSdust.txt.gz 2016-03-18 11:11 68M
refGene.sql 2020-05-05 16:36 1.9K
refGene.txt.gz 2020-05-05 16:36 158
refFlat.sql 2020-05-05 16:36 1.7K
refFlat.txt.gz 2020-05-05 16:36 140
all_mrna.sql 2020-05-05 21:19 2.1K
all_mrna.txt.gz 2020-05-05 21:19 514
mrnaOrientInfo.sql 2020-05-05 21:19 1.8K
mrnaOrientInfo.txt.gz 2020-05-05 21:19 210
xenoRefGene.sql 2020-08-18 06:44 2.0K
xenoRefGene.txt.gz 2020-08-18 06:44 30M
xenoRefFlat.sql 2020-08-18 06:44 1.7K
xenoRefFlat.txt.gz 2020-08-18 06:44 28M
xenoRefSeqAli.sql 2020-08-18 06:44 2.1K
xenoRefSeqAli.txt.gz 2020-08-18 06:44 27M
gbLoaded.sql 2020-08-18 06:44 1.6K
gbLoaded.txt.gz 2020-08-18 06:44 46K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 28K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 591
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 4.2K
tableList.sql 2024-11-17 03:35 1.6K
tableList.txt.gz 2024-11-17 03:35 1.8K
bigFiles.sql 2024-11-17 03:35 1.4K
bigFiles.txt.gz 2024-11-17 03:35 69