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 - all_mrna.sql 2016-05-15 08:49 2.1K all_mrna.txt.gz 2016-05-15 08:49 110 augustusGene.sql 2015-07-26 13:54 1.9K augustusGene.txt.gz 2015-07-26 13:54 1.4M bigFiles.sql 2021-05-02 03:11 1.4K bigFiles.txt.gz 2021-05-02 03:11 94 chainGalGal4.sql 2012-08-14 16:59 1.7K chainGalGal4.txt.gz 2012-08-14 17:00 89M chainGalGal4Link.sql 2012-08-14 16:52 1.6K chainGalGal4Link.txt.gz 2012-08-14 16:53 578M 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 chainHg19.sql 2012-08-14 17:00 1.7K chainHg19.txt.gz 2012-08-14 17:00 8.9M chainHg19Link.sql 2012-08-14 16:55 1.5K chainHg19Link.txt.gz 2012-08-14 16:55 50M chainMelGal1.sql 2012-08-14 16:58 1.7K chainMelGal1.txt.gz 2012-08-14 16:58 40M chainMelGal1Link.sql 2012-08-14 16:57 1.6K chainMelGal1Link.txt.gz 2012-08-14 16:57 273M 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 chainMelUnd1.sql 2012-11-25 14:17 1.7K chainMelUnd1.txt.gz 2012-11-25 14:17 96M chainMelUnd1Link.sql 2012-11-25 14:14 1.6K chainMelUnd1Link.txt.gz 2012-11-25 14:15 567M chainMm10.sql 2012-08-14 16:59 1.7K chainMm10.txt.gz 2012-08-14 16:59 6.1M chainMm10Link.sql 2012-08-14 16:56 1.5K chainMm10Link.txt.gz 2012-08-14 16:56 43M chainTaeGut1.sql 2012-08-14 16:59 1.7K chainTaeGut1.txt.gz 2012-08-14 16:59 224M chainTaeGut1Link.sql 2012-08-14 17:01 1.6K chainTaeGut1Link.txt.gz 2012-08-14 17:03 1.1G chromAlias.sql 2018-02-18 06:38 1.4K chromAlias.txt.gz 2018-02-18 06:38 245K chromInfo.sql 2012-08-14 16:55 1.4K chromInfo.txt.gz 2012-08-14 16:55 83K cpgIslandExt.sql 2012-08-14 16:55 1.7K cpgIslandExt.txt.gz 2012-08-14 16:55 281K cpgIslandExtUnmasked.sql 2014-06-01 13:37 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:37 373K cytoBandIdeo.sql 2013-04-28 15:37 1.5K cytoBandIdeo.txt.gz 2013-04-28 15:37 69K ensGene.sql 2020-09-01 09:38 1.9K ensGene.txt.gz 2020-09-01 09:38 1.7M ensGtp.sql 2020-09-01 09:38 1.4K ensGtp.txt.gz 2020-09-01 09:38 207K ensPep.sql 2020-09-01 11:12 1.3K ensPep.txt.gz 2020-09-01 11:12 5.3M ensemblSource.sql 2020-09-01 11:12 1.4K ensemblSource.txt.gz 2020-09-01 11:12 60K ensemblToGeneName.sql 2020-09-01 09:38 1.4K ensemblToGeneName.txt.gz 2020-09-01 09:38 104K extFile.sql 2012-08-14 16:56 1.4K extFile.txt.gz 2012-08-14 16:56 79 extNcbiRefSeq.sql 2020-05-10 03:27 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:27 90 gap.sql 2012-08-14 17:07 1.6K gap.txt.gz 2012-08-14 17:07 862K gbLoaded.sql 2020-08-19 11:56 1.6K gbLoaded.txt.gz 2020-08-19 11:56 15K gc5BaseBw.sql 2012-08-14 17:07 1.3K gc5BaseBw.txt.gz 2012-08-14 17:07 63 genscan.sql 2012-08-14 16:59 1.7K genscan.txt.gz 2012-08-14 16:59 1.2M genscanSubopt.sql 2012-08-14 17:00 1.6K genscanSubopt.txt.gz 2012-08-14 17:00 2.8M gold.sql 2012-08-14 16:58 1.7K gold.txt.gz 2012-08-14 16:58 1.3M grp.sql 2014-03-02 03:41 1.3K grp.txt.gz 2014-03-02 03:41 208 hgFindSpec.sql 2020-12-06 08:02 1.7K hgFindSpec.txt.gz 2020-12-06 08:02 1.1K history.sql 2012-08-14 16:59 1.6K history.txt.gz 2012-08-14 16:59 1.3K microsat.sql 2015-08-23 17:10 1.5K microsat.txt.gz 2015-08-23 17:10 16K mrnaOrientInfo.sql 2016-05-15 08:49 1.8K mrnaOrientInfo.txt.gz 2016-05-15 08:49 79 multiz7way.sql 2012-08-14 16:56 1.5K multiz7way.txt.gz 2012-08-14 16:56 50M multiz7wayFrames.sql 2012-08-14 16:55 1.7K multiz7wayFrames.txt.gz 2012-08-14 16:55 10M multiz7waySummary.sql 2012-08-14 16:59 1.6K multiz7waySummary.txt.gz 2012-08-14 16:59 4.2M 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 ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 1.8M ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.1M nestedRepeats.sql 2012-08-14 17:01 1.9K nestedRepeats.txt.gz 2012-08-14 17:01 378K netGalGal4.sql 2012-08-14 17:00 2.1K netGalGal4.txt.gz 2012-08-14 17:00 36M netGalGal6.sql 2019-01-20 19:40 2.1K netGalGal6.txt.gz 2019-01-20 19:40 40M netHg19.sql 2012-08-14 16:58 2.1K netHg19.txt.gz 2012-08-14 16:58 7.2M netMelGal1.sql 2012-08-14 16:58 2.1K netMelGal1.txt.gz 2012-08-14 16:58 36M netMelGal5.sql 2017-03-19 23:08 2.1K netMelGal5.txt.gz 2017-03-19 23:09 37M netMelUnd1.sql 2012-11-25 14:17 2.1K netMelUnd1.txt.gz 2012-11-25 14:17 29M netMm10.sql 2012-08-14 17:01 2.1K netMm10.txt.gz 2012-08-14 17:01 7.6M netTaeGut1.sql 2012-08-14 16:58 2.1K netTaeGut1.txt.gz 2012-08-14 16:58 17M phastCons7way.sql 2012-08-14 17:00 1.8K phastCons7way.txt.gz 2012-08-14 17:00 28M phastCons7wayBirds.sql 2012-08-14 16:55 1.8K phastCons7wayBirds.txt.gz 2012-08-14 16:55 28M phastCons7wayVertebrate.sql 2012-08-14 16:56 1.8K phastCons7wayVertebrate.txt.gz 2012-08-14 16:56 20M phastConsElements7way.sql 2012-08-14 17:07 1.6K phastConsElements7way.txt.gz 2012-08-14 17:07 4.1M phastConsElements7wayBirds.sql 2012-08-14 16:56 1.6K phastConsElements7wayBirds.txt.gz 2012-08-14 16:56 3.2M phastConsElements7wayVertebrate.sql 2012-08-14 17:07 1.6K phastConsElements7wayVertebrate.txt.gz 2012-08-14 17:07 1.8M phyloP7way.sql 2012-08-14 17:07 1.8K phyloP7way.txt.gz 2012-08-14 17:07 30M phyloP7wayBirds.sql 2012-08-14 16:56 1.8K phyloP7wayBirds.txt.gz 2012-08-14 16:56 30M phyloP7wayVertebrate.sql 2012-08-14 16:55 1.8K phyloP7wayVertebrate.txt.gz 2012-08-14 16:55 20M rmsk.sql 2012-08-14 16:56 1.9K rmsk.txt.gz 2012-08-14 16:56 9.6M seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 345K simpleRepeat.sql 2012-08-14 16:55 1.9K simpleRepeat.txt.gz 2012-08-14 16:55 9.5M tableDescriptions.sql 2020-09-30 02:04 1.4K tableDescriptions.txt.gz 2020-09-30 02:04 7.5K tableList.sql 2021-05-02 03:11 1.6K tableList.txt.gz 2021-05-02 03:11 4.4K trackDb.sql 2020-12-06 08:02 2.0K trackDb.txt.gz 2020-12-06 08:02 50K ucscToINSDC.sql 2013-09-15 13:30 1.4K ucscToINSDC.txt.gz 2013-09-15 13:30 131K ucscToRefSeq.sql 2018-02-18 06:38 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:38 139K windowmaskerSdust.sql 2012-08-14 17:01 1.5K windowmaskerSdust.txt.gz 2012-08-14 17:01 59M xenoRefFlat.sql 2020-08-19 11:56 1.7K xenoRefFlat.txt.gz 2020-08-19 11:56 25M xenoRefGene.sql 2020-08-19 11:56 1.9K xenoRefGene.txt.gz 2020-08-19 11:56 28M xenoRefSeqAli.sql 2020-08-19 11:56 2.1K xenoRefSeqAli.txt.gz 2020-08-19 11:56 25M