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