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 2012-08-14 16:52 1.6K
chainGalGal4Link.txt.gz 2012-08-14 16:53 578M
cpgIslandExt.sql 2012-08-14 16:55 1.7K
cpgIslandExt.txt.gz 2012-08-14 16:55 281K
phyloP7wayVertebrate.sql 2012-08-14 16:55 1.8K
phyloP7wayVertebrate.txt.gz 2012-08-14 16:55 20M
simpleRepeat.sql 2012-08-14 16:55 1.9K
simpleRepeat.txt.gz 2012-08-14 16:55 9.5M
chromInfo.sql 2012-08-14 16:55 1.4K
chromInfo.txt.gz 2012-08-14 16:55 83K
phastCons7wayBirds.sql 2012-08-14 16:55 1.8K
phastCons7wayBirds.txt.gz 2012-08-14 16:55 28M
multiz7wayFrames.sql 2012-08-14 16:55 1.7K
multiz7wayFrames.txt.gz 2012-08-14 16:55 10M
chainHg19Link.sql 2012-08-14 16:55 1.5K
chainHg19Link.txt.gz 2012-08-14 16:55 50M
extFile.sql 2012-08-14 16:56 1.4K
extFile.txt.gz 2012-08-14 16:56 79
phastConsElements7wayBirds.sql 2012-08-14 16:56 1.6K
phastConsElements7wayBirds.txt.gz 2012-08-14 16:56 3.2M
rmsk.sql 2012-08-14 16:56 1.9K
rmsk.txt.gz 2012-08-14 16:56 9.6M
multiz7way.sql 2012-08-14 16:56 1.5K
multiz7way.txt.gz 2012-08-14 16:56 50M
chainMm10Link.sql 2012-08-14 16:56 1.5K
chainMm10Link.txt.gz 2012-08-14 16:56 43M
phyloP7wayBirds.sql 2012-08-14 16:56 1.8K
phyloP7wayBirds.txt.gz 2012-08-14 16:56 30M
phastCons7wayVertebrate.sql 2012-08-14 16:56 1.8K
phastCons7wayVertebrate.txt.gz 2012-08-14 16:56 20M
chainMelGal1Link.sql 2012-08-14 16:57 1.6K
chainMelGal1Link.txt.gz 2012-08-14 16:57 273M
netMelGal1.sql 2012-08-14 16:58 2.1K
netMelGal1.txt.gz 2012-08-14 16:58 36M
netHg19.sql 2012-08-14 16:58 2.1K
netHg19.txt.gz 2012-08-14 16:58 7.2M
gold.sql 2012-08-14 16:58 1.7K
gold.txt.gz 2012-08-14 16:58 1.3M
netTaeGut1.sql 2012-08-14 16:58 2.1K
netTaeGut1.txt.gz 2012-08-14 16:58 17M
chainMelGal1.sql 2012-08-14 16:58 1.7K
chainMelGal1.txt.gz 2012-08-14 16:58 40M
multiz7waySummary.sql 2012-08-14 16:59 1.6K
multiz7waySummary.txt.gz 2012-08-14 16:59 4.2M
chainTaeGut1.sql 2012-08-14 16:59 1.7K
chainTaeGut1.txt.gz 2012-08-14 16:59 224M
chainMm10.sql 2012-08-14 16:59 1.7K
chainMm10.txt.gz 2012-08-14 16:59 6.1M
chainGalGal4.sql 2012-08-14 16:59 1.7K
genscan.sql 2012-08-14 16:59 1.7K
genscan.txt.gz 2012-08-14 16:59 1.2M
history.sql 2012-08-14 16:59 1.6K
history.txt.gz 2012-08-14 16:59 1.3K
chainGalGal4.txt.gz 2012-08-14 17:00 89M
phastCons7way.sql 2012-08-14 17:00 1.8K
phastCons7way.txt.gz 2012-08-14 17:00 28M
genscanSubopt.sql 2012-08-14 17:00 1.6K
genscanSubopt.txt.gz 2012-08-14 17:00 2.8M
netGalGal4.sql 2012-08-14 17:00 2.1K
netGalGal4.txt.gz 2012-08-14 17:00 36M
chainHg19.sql 2012-08-14 17:00 1.7K
chainHg19.txt.gz 2012-08-14 17:00 8.9M
netMm10.sql 2012-08-14 17:01 2.1K
netMm10.txt.gz 2012-08-14 17:01 7.6M
nestedRepeats.sql 2012-08-14 17:01 1.9K
nestedRepeats.txt.gz 2012-08-14 17:01 378K
windowmaskerSdust.sql 2012-08-14 17:01 1.5K
windowmaskerSdust.txt.gz 2012-08-14 17:01 59M
chainTaeGut1Link.sql 2012-08-14 17:01 1.6K
chainTaeGut1Link.txt.gz 2012-08-14 17:03 1.1G
phyloP7way.sql 2012-08-14 17:07 1.8K
phyloP7way.txt.gz 2012-08-14 17:07 30M
phastConsElements7wayVertebrate.sql 2012-08-14 17:07 1.6K
phastConsElements7way.sql 2012-08-14 17:07 1.6K
phastConsElements7way.txt.gz 2012-08-14 17:07 4.1M
phastConsElements7wayVertebrate.txt.gz 2012-08-14 17:07 1.8M
gap.sql 2012-08-14 17:07 1.6K
gap.txt.gz 2012-08-14 17:07 862K
gc5BaseBw.sql 2012-08-14 17:07 1.3K
gc5BaseBw.txt.gz 2012-08-14 17:07 63
chainMelUnd1Link.sql 2012-11-25 14:14 1.6K
chainMelUnd1Link.txt.gz 2012-11-25 14:15 567M
netMelUnd1.sql 2012-11-25 14:17 2.1K
netMelUnd1.txt.gz 2012-11-25 14:17 29M
chainMelUnd1.sql 2012-11-25 14:17 1.7K
chainMelUnd1.txt.gz 2012-11-25 14:17 96M
cytoBandIdeo.sql 2013-04-28 15:37 1.5K
cytoBandIdeo.txt.gz 2013-04-28 15:37 69K
ucscToINSDC.sql 2013-09-15 13:30 1.4K
ucscToINSDC.txt.gz 2013-09-15 13:30 131K
grp.sql 2014-03-02 03:41 1.3K
grp.txt.gz 2014-03-02 03:41 208
cpgIslandExtUnmasked.sql 2014-06-01 13:37 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 13:37 373K
augustusGene.sql 2015-07-26 13:54 1.9K
augustusGene.txt.gz 2015-07-26 13:54 1.4M
microsat.sql 2015-08-23 17:10 1.5K
microsat.txt.gz 2015-08-23 17:10 16K
all_mrna.sql 2016-05-15 08:49 2.1K
all_mrna.txt.gz 2016-05-15 08:49 110
mrnaOrientInfo.sql 2016-05-15 08:49 1.8K
mrnaOrientInfo.txt.gz 2016-05-15 08:49 79
chainMelGal5.sql 2017-03-19 22:42 1.7K
chainMelGal5.txt.gz 2017-03-19 22:42 95M
chainMelGal5Link.sql 2017-03-19 22:44 1.5K
chainMelGal5Link.txt.gz 2017-03-19 22:50 631M
netMelGal5.sql 2017-03-19 23:08 2.1K
netMelGal5.txt.gz 2017-03-19 23:09 37M
chromAlias.sql 2018-02-18 06:38 1.4K
chromAlias.txt.gz 2018-02-18 06:38 245K
ucscToRefSeq.sql 2018-02-18 06:38 1.4K
ucscToRefSeq.txt.gz 2018-02-18 06:38 139K
chainGalGal6.sql 2019-01-20 19:25 1.7K
chainGalGal6.txt.gz 2019-01-20 19:25 452M
chainGalGal6Link.sql 2019-01-20 19:26 1.5K
chainGalGal6Link.txt.gz 2019-01-20 19:30 2.6G
netGalGal6.sql 2019-01-20 19:40 2.1K
netGalGal6.txt.gz 2019-01-20 19:40 40M
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 90
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:27 1.8M
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 134K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 405
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 698K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 5.6M
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.1M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 1.8M
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 345K
xenoRefGene.sql 2020-08-19 11:56 2.0K
xenoRefGene.txt.gz 2020-08-19 11:56 28M
xenoRefFlat.sql 2020-08-19 11:56 1.7K
xenoRefFlat.txt.gz 2020-08-19 11:56 25M
xenoRefSeqAli.sql 2020-08-19 11:56 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 11:56 25M
gbLoaded.sql 2020-08-19 11:56 1.6K
gbLoaded.txt.gz 2020-08-19 11:56 15K
ensGene.sql 2021-05-25 14:32 1.9K
ensGene.txt.gz 2021-05-25 14:32 1.7M
ensGtp.sql 2021-05-25 14:32 1.4K
ensGtp.txt.gz 2021-05-25 14:32 207K
ensemblToGeneName.sql 2021-05-25 14:32 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:32 104K
ensemblSource.sql 2021-05-25 14:35 1.4K
ensemblSource.txt.gz 2021-05-25 14:35 60K
ensPep.sql 2021-05-25 14:35 1.3K
ensPep.txt.gz 2021-05-25 14:35 5.3M
trackDb_pushedout.sql 2023-12-05 13:50 2.1K
trackDb_pushedout.txt.gz 2023-12-05 13:50 40K
hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.2K
trackDb.sql 2024-01-31 15:13 2.1K
trackDb.txt.gz 2024-01-31 15:13 56K
hgFindSpec.sql 2024-01-31 15:13 1.8K
hgFindSpec.txt.gz 2024-01-31 15:13 1.2K
tableDescriptions.sql 2024-04-13 02:03 1.5K
tableDescriptions.txt.gz 2024-04-13 02:03 7.5K
tableList.sql 2024-04-14 03:34 1.6K
tableList.txt.gz 2024-04-14 03:34 4.6K
bigFiles.sql 2024-04-14 03:34 1.4K
bigFiles.txt.gz 2024-04-14 03:34 94