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.

---------------------------------------------------------------
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.

-----------------------------------------------------------------------------
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 2024-02-24 02:03 1.4K tableDescriptions.txt.gz 2024-02-24 02:03 7.5K tableList.sql 2024-02-25 03:46 1.6K tableList.txt.gz 2024-02-25 03:46 4.6K bigFiles.sql 2024-02-25 03:46 1.4K bigFiles.txt.gz 2024-02-25 03:46 94