This directory contains a dump of the UCSC genome annotation database for the
    Feb. 2013 (WashU taeGut324/taeGut2) assembly of the zebra finch genome
    (taeGut2, Washington University School of Medicine) .

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/367
    http://www.ncbi.nlm.nih.gov/genome/assembly/524908
    http://www.ncbi.nlm.nih.gov/bioproject/17289

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=taeGut2
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/taeGut2/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/taeGut2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/database/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut2/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 taeGut2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql taeGut2 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Zebra finch sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, with
the following understanding:

1. The data may be freely downloaded, used in analyses, and repackaged in
   databases.

2. Users are free to use the data in scientific papers analyzing these data
   if the providers of these data are properly acknowledged.  See
   http://genome.ucsc.edu/goldenPath/credits.html for credit information.

3. The centers producing the data reserve the right to publish the initial
   large-scale analyses of the data set, including large-scale identification
   of regions of evolutionary conservation and large-scale genomic assembly.
   Large-scale refers to regions with size on the order of a chromosome (that
   is, 30 Mb or more).

4. Any redistribution of the data should carry this notice.

-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.

      Name                        Last modified      Size  Description
Parent Directory - gc5BaseBw.txt.gz 2014-05-08 12:16 66 ncbiRefSeqOther.txt.gz 2018-08-14 02:31 75 extNcbiRefSeq.txt.gz 2018-08-14 02:31 90 bigFiles.txt.gz 2022-08-07 03:10 95 grp.txt.gz 2014-05-08 12:16 206 hgFindSpec.txt.gz 2021-08-10 17:30 1.0K gc5BaseBw.sql 2014-05-08 12:16 1.3K ncbiRefSeqOther.sql 2018-08-14 02:31 1.3K grp.sql 2014-05-08 12:16 1.3K ncbiRefSeqCds.sql 2018-08-14 02:31 1.4K bigFiles.sql 2022-08-07 03:10 1.4K ncbiRefSeqPepTable.sql 2018-08-14 02:31 1.4K chromInfo.sql 2014-05-08 12:16 1.4K extFile.sql 2014-05-08 12:16 1.4K chromAlias.sql 2018-02-18 08:49 1.4K tableDescriptions.sql 2021-08-07 06:33 1.4K ucscToINSDC.sql 2014-05-08 12:16 1.4K ucscToRefSeq.sql 2018-02-18 08:49 1.4K extNcbiRefSeq.sql 2018-08-14 02:31 1.5K microsat.sql 2015-08-24 02:22 1.5K windowmaskerSdust.sql 2014-05-08 12:16 1.5K cytoBandIdeo.sql 2014-05-08 12:16 1.5K chainHg19Link.sql 2014-05-08 12:12 1.5K chainGalGal4Link.sql 2014-05-08 12:11 1.5K chainGalGal6Link.sql 2019-01-20 20:22 1.5K chainMelGal5Link.sql 2017-03-21 06:23 1.5K tableList.sql 2022-08-07 03:10 1.6K seqNcbiRefSeq.sql 2018-08-14 02:31 1.6K history.sql 2014-05-08 12:10 1.6K gbLoaded.sql 2020-08-20 13:18 1.6K gap.sql 2014-05-08 12:16 1.6K gold.sql 2014-05-08 12:16 1.7K genscan.sql 2014-05-08 12:16 1.7K cpgIslandExt.sql 2014-05-08 12:16 1.7K chainHg19.sql 2014-05-08 12:12 1.7K refFlat.sql 2020-08-20 13:02 1.7K chainGalGal4.sql 2014-05-08 12:11 1.7K chainGalGal6.sql 2019-01-20 20:21 1.7K chainMelGal5.sql 2017-03-21 06:35 1.7K cpgIslandExtUnmasked.sql 2014-05-08 12:16 1.7K xenoRefFlat.sql 2020-08-20 13:02 1.7K hgFindSpec.sql 2021-08-10 17:30 1.8K estOrientInfo.sql 2014-05-08 12:16 1.8K mrnaOrientInfo.sql 2020-08-20 13:02 1.8K rmsk.sql 2014-05-08 12:16 1.9K refGene.sql 2020-08-20 13:02 1.9K simpleRepeat.sql 2014-05-08 12:16 1.9K nestedRepeats.sql 2014-05-08 12:16 1.9K xenoRefGene.sql 2020-08-20 13:02 1.9K augustusGene.sql 2015-07-26 17:28 1.9K ncbiRefSeq.sql 2018-02-09 13:48 2.0K ncbiRefSeqCurated.sql 2018-02-09 13:48 2.0K ncbiRefSeqPredicted.sql 2018-02-09 13:48 2.0K ncbiRefSeqLink.sql 2018-02-09 13:48 2.0K trackDb.sql 2021-08-10 17:30 2.1K netHg19.sql 2014-05-08 12:16 2.1K netGalGal4.sql 2014-05-08 12:16 2.1K netGalGal6.sql 2019-01-20 20:21 2.1K netMelGal5.sql 2017-03-21 06:36 2.1K all_est.sql 2014-05-08 12:10 2.1K all_mrna.sql 2018-10-21 09:15 2.1K intronEst.sql 2014-05-08 12:10 2.1K refSeqAli.sql 2020-08-20 13:02 2.1K xenoRefSeqAli.sql 2020-08-20 13:18 2.1K ncbiRefSeqPsl.sql 2018-02-09 13:48 2.1K tableList.txt.gz 2022-08-07 03:10 3.4K tableDescriptions.txt.gz 2021-08-07 06:33 6.2K microsat.txt.gz 2015-08-24 02:22 38K trackDb.txt.gz 2021-08-10 17:30 44K gbLoaded.txt.gz 2020-08-20 13:18 62K ncbiRefSeqCurated.txt.gz 2018-02-09 13:48 75K refFlat.txt.gz 2020-08-20 13:02 75K mrnaOrientInfo.txt.gz 2020-08-20 13:02 76K refGene.txt.gz 2020-08-20 13:02 84K refSeqAli.txt.gz 2020-08-20 13:02 89K ncbiRefSeqCds.txt.gz 2018-08-14 02:31 122K cytoBandIdeo.txt.gz 2014-05-08 12:16 197K chromInfo.txt.gz 2014-05-08 12:16 201K all_mrna.txt.gz 2018-10-21 09:15 245K ucscToINSDC.txt.gz 2014-05-08 12:16 293K ucscToRefSeq.txt.gz 2018-02-18 08:49 302K seqNcbiRefSeq.txt.gz 2018-08-14 02:31 315K chromAlias.txt.gz 2018-02-18 08:49 380K extFile.txt.gz 2014-05-08 12:16 385K nestedRepeats.txt.gz 2014-05-08 12:16 498K history.txt.gz 2014-05-08 12:10 527K cpgIslandExt.txt.gz 2014-05-08 12:16 573K cpgIslandExtUnmasked.txt.gz 2014-05-08 12:16 645K ncbiRefSeqLink.txt.gz 2018-02-09 13:48 706K gap.txt.gz 2014-05-08 12:16 913K estOrientInfo.txt.gz 2014-05-08 12:16 1.1M ncbiRefSeqPredicted.txt.gz 2018-02-09 13:48 1.7M ncbiRefSeq.txt.gz 2018-02-09 13:48 1.8M gold.txt.gz 2014-05-08 12:16 1.9M augustusGene.txt.gz 2015-07-26 17:28 1.9M ncbiRefSeqPsl.txt.gz 2018-02-09 13:48 1.9M intronEst.txt.gz 2014-05-08 12:10 2.1M genscan.txt.gz 2014-05-08 12:16 2.9M all_est.txt.gz 2014-05-08 12:10 4.0M ncbiRefSeqPepTable.txt.gz 2018-08-14 02:31 5.4M simpleRepeat.txt.gz 2014-05-08 12:16 9.3M netHg19.txt.gz 2014-05-08 12:16 13M rmsk.txt.gz 2014-05-08 12:16 14M chainGalGal4.txt.gz 2014-05-08 12:11 17M chainMelGal5.txt.gz 2017-03-21 06:35 20M xenoRefSeqAli.txt.gz 2020-08-20 13:18 21M xenoRefFlat.txt.gz 2020-08-20 13:02 21M xenoRefGene.txt.gz 2020-08-20 13:02 23M netGalGal4.txt.gz 2014-05-08 12:16 38M netMelGal5.txt.gz 2017-03-21 06:36 42M netGalGal6.txt.gz 2019-01-20 20:21 42M windowmaskerSdust.txt.gz 2014-05-08 12:16 67M chainGalGal6.txt.gz 2019-01-20 20:21 70M chainHg19.txt.gz 2014-05-08 12:12 142M chainGalGal4Link.txt.gz 2014-05-08 12:11 223M chainMelGal5Link.txt.gz 2017-03-21 06:24 233M chainHg19Link.txt.gz 2014-05-08 12:13 400M chainGalGal6Link.txt.gz 2019-01-20 20:22 494M