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