This directory contains a dump of the UCSC genome annotation database for
the Apr. 2012 (GeoFor_1.0/geoFor1) assembly of the medium ground finch genome (geoFor1, Beijing Genomics Institute).
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/13302
http://www.ncbi.nlm.nih.gov/genome/assembly/402638
http://www.ncbi.nlm.nih.gov/bioproject/156703
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=geoFor1
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/geoFor1/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/geoFor1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/geoFor1/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 geoFor1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql geoFor1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
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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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Name Last modified Size Description
Parent Directory -
chainGalGal4Link.sql 14-Aug-2012 16:52 1.6K
chainGalGal4Link.txt.gz 14-Aug-2012 16:53 578M
cpgIslandExt.sql 14-Aug-2012 16:55 1.7K
cpgIslandExt.txt.gz 14-Aug-2012 16:55 281K
phyloP7wayVertebrate.sql 14-Aug-2012 16:55 1.8K
phyloP7wayVertebrate.txt.gz 14-Aug-2012 16:55 20M
simpleRepeat.sql 14-Aug-2012 16:55 1.9K
simpleRepeat.txt.gz 14-Aug-2012 16:55 9.5M
chromInfo.sql 14-Aug-2012 16:55 1.4K
chromInfo.txt.gz 14-Aug-2012 16:55 83K
phastCons7wayBirds.sql 14-Aug-2012 16:55 1.8K
phastCons7wayBirds.txt.gz 14-Aug-2012 16:55 28M
multiz7wayFrames.sql 14-Aug-2012 16:55 1.7K
multiz7wayFrames.txt.gz 14-Aug-2012 16:55 10M
chainHg19Link.sql 14-Aug-2012 16:55 1.5K
chainHg19Link.txt.gz 14-Aug-2012 16:55 50M
extFile.sql 14-Aug-2012 16:56 1.4K
extFile.txt.gz 14-Aug-2012 16:56 79
phastConsElements7wayBirds.sql 14-Aug-2012 16:56 1.6K
phastConsElements7wayBirds.txt.gz 14-Aug-2012 16:56 3.2M
rmsk.sql 14-Aug-2012 16:56 1.9K
rmsk.txt.gz 14-Aug-2012 16:56 9.6M
multiz7way.sql 14-Aug-2012 16:56 1.5K
multiz7way.txt.gz 14-Aug-2012 16:56 50M
chainMm10Link.sql 14-Aug-2012 16:56 1.5K
chainMm10Link.txt.gz 14-Aug-2012 16:56 43M
phyloP7wayBirds.sql 14-Aug-2012 16:56 1.8K
phyloP7wayBirds.txt.gz 14-Aug-2012 16:56 30M
phastCons7wayVertebrate.sql 14-Aug-2012 16:56 1.8K
phastCons7wayVertebrate.txt.gz 14-Aug-2012 16:56 20M
chainMelGal1Link.sql 14-Aug-2012 16:57 1.6K
chainMelGal1Link.txt.gz 14-Aug-2012 16:57 273M
netMelGal1.sql 14-Aug-2012 16:58 2.1K
netMelGal1.txt.gz 14-Aug-2012 16:58 36M
netHg19.sql 14-Aug-2012 16:58 2.1K
netHg19.txt.gz 14-Aug-2012 16:58 7.2M
gold.sql 14-Aug-2012 16:58 1.7K
gold.txt.gz 14-Aug-2012 16:58 1.3M
netTaeGut1.sql 14-Aug-2012 16:58 2.1K
netTaeGut1.txt.gz 14-Aug-2012 16:58 17M
chainMelGal1.sql 14-Aug-2012 16:58 1.7K
chainMelGal1.txt.gz 14-Aug-2012 16:58 40M
multiz7waySummary.sql 14-Aug-2012 16:59 1.6K
multiz7waySummary.txt.gz 14-Aug-2012 16:59 4.2M
chainTaeGut1.sql 14-Aug-2012 16:59 1.7K
chainTaeGut1.txt.gz 14-Aug-2012 16:59 224M
chainMm10.sql 14-Aug-2012 16:59 1.7K
chainMm10.txt.gz 14-Aug-2012 16:59 6.1M
chainGalGal4.sql 14-Aug-2012 16:59 1.7K
genscan.sql 14-Aug-2012 16:59 1.7K
genscan.txt.gz 14-Aug-2012 16:59 1.2M
history.sql 14-Aug-2012 16:59 1.6K
history.txt.gz 14-Aug-2012 16:59 1.3K
chainGalGal4.txt.gz 14-Aug-2012 17:00 89M
phastCons7way.sql 14-Aug-2012 17:00 1.8K
phastCons7way.txt.gz 14-Aug-2012 17:00 28M
genscanSubopt.sql 14-Aug-2012 17:00 1.6K
genscanSubopt.txt.gz 14-Aug-2012 17:00 2.8M
netGalGal4.sql 14-Aug-2012 17:00 2.1K
netGalGal4.txt.gz 14-Aug-2012 17:00 36M
chainHg19.sql 14-Aug-2012 17:00 1.7K
chainHg19.txt.gz 14-Aug-2012 17:00 8.9M
netMm10.sql 14-Aug-2012 17:01 2.1K
netMm10.txt.gz 14-Aug-2012 17:01 7.6M
nestedRepeats.sql 14-Aug-2012 17:01 1.9K
nestedRepeats.txt.gz 14-Aug-2012 17:01 378K
windowmaskerSdust.sql 14-Aug-2012 17:01 1.5K
windowmaskerSdust.txt.gz 14-Aug-2012 17:01 59M
chainTaeGut1Link.sql 14-Aug-2012 17:01 1.6K
chainTaeGut1Link.txt.gz 14-Aug-2012 17:03 1.1G
phyloP7way.sql 14-Aug-2012 17:07 1.8K
phyloP7way.txt.gz 14-Aug-2012 17:07 30M
phastConsElements7wayVertebrate.sql 14-Aug-2012 17:07 1.6K
phastConsElements7way.sql 14-Aug-2012 17:07 1.6K
phastConsElements7way.txt.gz 14-Aug-2012 17:07 4.1M
phastConsElements7wayVertebrate.txt.gz 14-Aug-2012 17:07 1.8M
gap.sql 14-Aug-2012 17:07 1.6K
gap.txt.gz 14-Aug-2012 17:07 862K
gc5BaseBw.sql 14-Aug-2012 17:07 1.3K
gc5BaseBw.txt.gz 14-Aug-2012 17:07 63
chainMelUnd1Link.sql 25-Nov-2012 14:14 1.6K
chainMelUnd1Link.txt.gz 25-Nov-2012 14:15 567M
netMelUnd1.sql 25-Nov-2012 14:17 2.1K
netMelUnd1.txt.gz 25-Nov-2012 14:17 29M
chainMelUnd1.sql 25-Nov-2012 14:17 1.7K
chainMelUnd1.txt.gz 25-Nov-2012 14:17 96M
cytoBandIdeo.sql 28-Apr-2013 15:37 1.5K
cytoBandIdeo.txt.gz 28-Apr-2013 15:37 69K
ucscToINSDC.sql 15-Sep-2013 13:30 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 13:30 131K
grp.sql 02-Mar-2014 03:41 1.3K
grp.txt.gz 02-Mar-2014 03:41 208
cpgIslandExtUnmasked.sql 01-Jun-2014 13:37 1.7K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 13:37 373K
augustusGene.sql 26-Jul-2015 13:54 1.9K
augustusGene.txt.gz 26-Jul-2015 13:54 1.4M
microsat.sql 23-Aug-2015 17:10 1.5K
microsat.txt.gz 23-Aug-2015 17:10 16K
all_mrna.sql 15-May-2016 08:49 2.1K
all_mrna.txt.gz 15-May-2016 08:49 110
mrnaOrientInfo.sql 15-May-2016 08:49 1.8K
mrnaOrientInfo.txt.gz 15-May-2016 08:49 79
chainMelGal5.sql 19-Mar-2017 22:42 1.7K
chainMelGal5.txt.gz 19-Mar-2017 22:42 95M
chainMelGal5Link.sql 19-Mar-2017 22:44 1.5K
chainMelGal5Link.txt.gz 19-Mar-2017 22:50 631M
netMelGal5.sql 19-Mar-2017 23:08 2.1K
netMelGal5.txt.gz 19-Mar-2017 23:09 37M
xenoRefSeqAli.sql 09-Jul-2017 09:26 2.1K
xenoRefSeqAli.txt.gz 09-Jul-2017 09:26 19M
xenoRefFlat.sql 09-Jul-2017 09:27 1.7K
xenoRefFlat.txt.gz 09-Jul-2017 09:27 21M
gbLoaded.sql 09-Jul-2017 09:27 1.6K
gbLoaded.txt.gz 09-Jul-2017 09:27 5.6K
xenoRefGene.sql 09-Jul-2017 09:27 1.9K
xenoRefGene.txt.gz 09-Jul-2017 09:27 24M
hgFindSpec.sql 16-Jul-2017 05:52 1.7K
hgFindSpec.txt.gz 16-Jul-2017 05:52 523
tableList.sql 16-Jul-2017 05:52 1.5K
tableList.txt.gz 16-Jul-2017 05:52 3.5K
tableDescriptions.sql 16-Jul-2017 05:52 1.4K
tableDescriptions.txt.gz 16-Jul-2017 05:52 5.5K
trackDb.sql 16-Jul-2017 05:52 2.0K
trackDb.txt.gz 16-Jul-2017 05:52 37K
bigFiles.sql 16-Jul-2017 05:52 1.4K
bigFiles.txt.gz 16-Jul-2017 05:52 68