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 - gc5BaseBw.txt.gz 2012-08-14 17:07 63 ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75 extFile.txt.gz 2012-08-14 16:56 79 mrnaOrientInfo.txt.gz 2016-05-15 08:49 79 extNcbiRefSeq.txt.gz 2020-05-10 03:27 90 bigFiles.txt.gz 2024-03-24 03:45 94 all_mrna.txt.gz 2016-05-15 08:49 110 grp.txt.gz 2014-03-02 03:41 208 ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 405 hgFindSpec.txt.gz 2024-01-31 15:13 1.2K hgFindSpec_pushedout.txt.gz 2023-12-05 13:50 1.2K gc5BaseBw.sql 2012-08-14 17:07 1.3K ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K history.txt.gz 2012-08-14 16:59 1.3K ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K ensPep.sql 2021-05-25 14:35 1.3K grp.sql 2014-03-02 03:41 1.3K ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K ensemblSource.sql 2021-05-25 14:35 1.4K bigFiles.sql 2024-03-24 03:45 1.4K chromInfo.sql 2012-08-14 16:55 1.4K ensemblToGeneName.sql 2021-05-25 14:32 1.4K extFile.sql 2012-08-14 16:56 1.4K chromAlias.sql 2018-02-18 06:38 1.4K ucscToINSDC.sql 2013-09-15 13:30 1.4K tableDescriptions.sql 2024-03-23 02:03 1.4K ucscToRefSeq.sql 2018-02-18 06:38 1.4K extNcbiRefSeq.sql 2020-05-10 03:27 1.4K ensGtp.sql 2021-05-25 14:32 1.4K microsat.sql 2015-08-23 17:10 1.5K windowmaskerSdust.sql 2012-08-14 17:01 1.5K cytoBandIdeo.sql 2013-04-28 15:37 1.5K multiz7way.sql 2012-08-14 16:56 1.5K chainHg19Link.sql 2012-08-14 16:55 1.5K chainMm10Link.sql 2012-08-14 16:56 1.5K chainGalGal6Link.sql 2019-01-20 19:26 1.5K chainMelGal5Link.sql 2017-03-19 22:44 1.5K seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K chainGalGal4Link.sql 2012-08-14 16:52 1.6K chainMelGal1Link.sql 2012-08-14 16:57 1.6K chainMelUnd1Link.sql 2012-11-25 14:14 1.6K chainTaeGut1Link.sql 2012-08-14 17:01 1.6K phastConsElements7way.sql 2012-08-14 17:07 1.6K tableList.sql 2024-03-24 03:45 1.6K genscanSubopt.sql 2012-08-14 17:00 1.6K phastConsElements7wayBirds.sql 2012-08-14 16:56 1.6K history.sql 2012-08-14 16:59 1.6K multiz7waySummary.sql 2012-08-14 16:59 1.6K phastConsElements7wayVertebrate.sql 2012-08-14 17:07 1.6K gap.sql 2012-08-14 17:07 1.6K gbLoaded.sql 2020-08-19 11:56 1.6K gold.sql 2012-08-14 16:58 1.7K genscan.sql 2012-08-14 16:59 1.7K cpgIslandExt.sql 2012-08-14 16:55 1.7K chainHg19.sql 2012-08-14 17:00 1.7K chainMm10.sql 2012-08-14 16:59 1.7K chainGalGal6.sql 2019-01-20 19:25 1.7K chainMelGal5.sql 2017-03-19 22:42 1.7K cpgIslandExtUnmasked.sql 2014-06-01 13:37 1.7K chainGalGal4.sql 2012-08-14 16:59 1.7K chainMelGal1.sql 2012-08-14 16:58 1.7K chainMelUnd1.sql 2012-11-25 14:17 1.7K chainTaeGut1.sql 2012-08-14 16:59 1.7K multiz7wayFrames.sql 2012-08-14 16:55 1.7K xenoRefFlat.sql 2020-08-19 11:56 1.7K hgFindSpec.sql 2024-01-31 15:13 1.8K phyloP7way.sql 2012-08-14 17:07 1.8K mrnaOrientInfo.sql 2016-05-15 08:49 1.8K phastCons7way.sql 2012-08-14 17:00 1.8K phyloP7wayBirds.sql 2012-08-14 16:56 1.8K hgFindSpec_pushedout.sql 2023-12-05 13:50 1.8K phastCons7wayBirds.sql 2012-08-14 16:55 1.8K phyloP7wayVertebrate.sql 2012-08-14 16:55 1.8K phastCons7wayVertebrate.sql 2012-08-14 16:56 1.8K rmsk.sql 2012-08-14 16:56 1.9K simpleRepeat.sql 2012-08-14 16:55 1.9K ncbiRefSeq.sql 2020-05-10 03:27 1.9K nestedRepeats.sql 2012-08-14 17:01 1.9K augustusGene.sql 2015-07-26 13:54 1.9K ensGene.sql 2021-05-25 14:32 1.9K ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K xenoRefGene.sql 2020-08-19 11:56 2.0K ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K trackDb.sql 2024-01-31 15:13 2.1K trackDb_pushedout.sql 2023-12-05 13:50 2.1K netHg19.sql 2012-08-14 16:58 2.1K netMm10.sql 2012-08-14 17:01 2.1K netGalGal6.sql 2019-01-20 19:40 2.1K netMelGal5.sql 2017-03-19 23:08 2.1K netGalGal4.sql 2012-08-14 17:00 2.1K netMelGal1.sql 2012-08-14 16:58 2.1K netMelUnd1.sql 2012-11-25 14:17 2.1K netTaeGut1.sql 2012-08-14 16:58 2.1K all_mrna.sql 2016-05-15 08:49 2.1K ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K xenoRefSeqAli.sql 2020-08-19 11:56 2.1K tableList.txt.gz 2024-03-24 03:45 4.6K tableDescriptions.txt.gz 2024-03-23 02:03 7.5K gbLoaded.txt.gz 2020-08-19 11:56 15K microsat.txt.gz 2015-08-23 17:10 16K trackDb_pushedout.txt.gz 2023-12-05 13:50 40K trackDb.txt.gz 2024-01-31 15:13 56K ensemblSource.txt.gz 2021-05-25 14:35 60K cytoBandIdeo.txt.gz 2013-04-28 15:37 69K chromInfo.txt.gz 2012-08-14 16:55 83K ensemblToGeneName.txt.gz 2021-05-25 14:32 104K ucscToINSDC.txt.gz 2013-09-15 13:30 131K ncbiRefSeqCds.txt.gz 2020-05-10 03:27 134K ucscToRefSeq.txt.gz 2018-02-18 06:38 139K ensGtp.txt.gz 2021-05-25 14:32 207K chromAlias.txt.gz 2018-02-18 06:38 245K cpgIslandExt.txt.gz 2012-08-14 16:55 281K seqNcbiRefSeq.txt.gz 2020-05-10 03:27 345K cpgIslandExtUnmasked.txt.gz 2014-06-01 13:37 373K nestedRepeats.txt.gz 2012-08-14 17:01 378K ncbiRefSeqLink.txt.gz 2020-05-10 03:27 698K gap.txt.gz 2012-08-14 17:07 862K genscan.txt.gz 2012-08-14 16:59 1.2M gold.txt.gz 2012-08-14 16:58 1.3M augustusGene.txt.gz 2015-07-26 13:54 1.4M ensGene.txt.gz 2021-05-25 14:32 1.7M ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 1.8M ncbiRefSeq.txt.gz 2020-05-10 03:27 1.8M phastConsElements7wayVertebrate.txt.gz 2012-08-14 17:07 1.8M ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.1M genscanSubopt.txt.gz 2012-08-14 17:00 2.8M phastConsElements7wayBirds.txt.gz 2012-08-14 16:56 3.2M phastConsElements7way.txt.gz 2012-08-14 17:07 4.1M multiz7waySummary.txt.gz 2012-08-14 16:59 4.2M ensPep.txt.gz 2021-05-25 14:35 5.3M ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 5.6M chainMm10.txt.gz 2012-08-14 16:59 6.1M netHg19.txt.gz 2012-08-14 16:58 7.2M netMm10.txt.gz 2012-08-14 17:01 7.6M chainHg19.txt.gz 2012-08-14 17:00 8.9M simpleRepeat.txt.gz 2012-08-14 16:55 9.5M rmsk.txt.gz 2012-08-14 16:56 9.6M multiz7wayFrames.txt.gz 2012-08-14 16:55 10M netTaeGut1.txt.gz 2012-08-14 16:58 17M phyloP7wayVertebrate.txt.gz 2012-08-14 16:55 20M phastCons7wayVertebrate.txt.gz 2012-08-14 16:56 20M xenoRefSeqAli.txt.gz 2020-08-19 11:56 25M xenoRefFlat.txt.gz 2020-08-19 11:56 25M xenoRefGene.txt.gz 2020-08-19 11:56 28M phastCons7wayBirds.txt.gz 2012-08-14 16:55 28M phastCons7way.txt.gz 2012-08-14 17:00 28M netMelUnd1.txt.gz 2012-11-25 14:17 29M phyloP7way.txt.gz 2012-08-14 17:07 30M phyloP7wayBirds.txt.gz 2012-08-14 16:56 30M netGalGal4.txt.gz 2012-08-14 17:00 36M netMelGal1.txt.gz 2012-08-14 16:58 36M netMelGal5.txt.gz 2017-03-19 23:09 37M netGalGal6.txt.gz 2019-01-20 19:40 40M chainMelGal1.txt.gz 2012-08-14 16:58 40M chainMm10Link.txt.gz 2012-08-14 16:56 43M multiz7way.txt.gz 2012-08-14 16:56 50M chainHg19Link.txt.gz 2012-08-14 16:55 50M windowmaskerSdust.txt.gz 2012-08-14 17:01 59M chainGalGal4.txt.gz 2012-08-14 17:00 89M chainMelGal5.txt.gz 2017-03-19 22:42 95M chainMelUnd1.txt.gz 2012-11-25 14:17 96M chainTaeGut1.txt.gz 2012-08-14 16:59 224M chainMelGal1Link.txt.gz 2012-08-14 16:57 273M chainGalGal6.txt.gz 2019-01-20 19:25 452M chainMelUnd1Link.txt.gz 2012-11-25 14:15 567M chainGalGal4Link.txt.gz 2012-08-14 16:53 578M chainMelGal5Link.txt.gz 2017-03-19 22:50 631M chainTaeGut1Link.txt.gz 2012-08-14 17:03 1.1G chainGalGal6Link.txt.gz 2019-01-20 19:30 2.6G