This directory contains a dump of the UCSC genome annotation database for
the Sep. 2011 (WUSTL v6.3/melUnd1) assembly of the budgerigar genome (melUnd1,
WUSTL Melopsittacus undulatus Budgerigar Version 6.3 (GCA_000238935.1)).
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/10765
    http://www.ncbi.nlm.nih.gov/genome/assembly/325078
    http://www.ncbi.nlm.nih.gov/bioproject/72527

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=melUnd1
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/melUnd1/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/melUnd1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/melUnd1/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melUnd1/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/melUnd1/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 melUnd1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql melUnd1 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'

The Budgerigar 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.

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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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All the files and tables in this directory are freely usable for any purpose.
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      Name                        Last modified      Size  Description
Parent Directory - all_mrna.sql 2018-11-04 07:31 2.1K all_mrna.txt.gz 2018-11-04 07:31 2.5K augustusGene.sql 2015-07-26 16:22 1.9K augustusGene.txt.gz 2015-07-26 16:22 1.4M bigFiles.sql 2021-05-02 03:12 1.4K bigFiles.txt.gz 2021-05-02 03:12 94 chainGalGal6.sql 2019-01-20 20:18 1.7K chainGalGal6.txt.gz 2019-01-20 20:18 352M chainGalGal6Link.sql 2019-01-20 20:08 1.5K chainGalGal6Link.txt.gz 2019-01-20 20:10 2.0G chainGeoFor1.sql 2012-11-06 14:21 1.7K chainGeoFor1.txt.gz 2012-11-06 14:21 97M chainGeoFor1Link.sql 2012-11-06 14:21 1.6K chainGeoFor1Link.txt.gz 2012-11-06 14:22 570M chainMm10.sql 2012-11-06 14:24 1.7K chainMm10.txt.gz 2012-11-06 14:24 4.9M chainMm10Link.sql 2012-11-06 14:20 1.5K chainMm10Link.txt.gz 2012-11-06 14:20 42M chromAlias.sql 2020-04-12 03:25 1.4K chromAlias.txt.gz 2020-04-12 03:25 244K chromInfo.sql 2012-11-06 14:20 1.4K chromInfo.txt.gz 2012-11-06 14:20 109K cpgIslandExt.sql 2012-11-06 14:24 1.7K cpgIslandExt.txt.gz 2012-11-06 14:24 302K cpgIslandExtUnmasked.sql 2014-06-01 16:20 1.7K cpgIslandExtUnmasked.txt.gz 2014-06-01 16:20 335K cytoBandIdeo.sql 2013-04-28 18:21 1.5K cytoBandIdeo.txt.gz 2013-04-28 18:21 113K ensGene.sql 2020-08-31 15:41 1.9K ensGene.txt.gz 2020-08-31 15:41 1.8M ensGtp.sql 2020-08-31 15:41 1.4K ensGtp.txt.gz 2020-08-31 15:41 223K ensPep.sql 2020-08-31 16:02 1.3K ensPep.txt.gz 2020-08-31 16:02 5.0M ensemblSource.sql 2020-08-31 16:02 1.4K ensemblSource.txt.gz 2020-08-31 16:02 70K ensemblToGeneName.sql 2020-08-31 15:41 1.4K ensemblToGeneName.txt.gz 2020-08-31 15:41 105K extNcbiRefSeq.sql 2020-05-10 03:28 1.4K extNcbiRefSeq.txt.gz 2020-05-10 03:28 90 gap.sql 2012-11-06 14:20 1.6K gap.txt.gz 2012-11-06 14:20 622K gbLoaded.sql 2020-08-19 17:01 1.6K gbLoaded.txt.gz 2020-08-19 17:01 14K gc5BaseBw.sql 2012-11-06 14:20 1.3K gc5BaseBw.txt.gz 2012-11-06 14:20 63 genscan.sql 2012-11-06 14:21 1.7K genscan.txt.gz 2012-11-06 14:21 1.4M gold.sql 2012-11-06 14:20 1.7K gold.txt.gz 2012-11-06 14:20 1.0M grp.sql 2014-03-02 04:14 1.3K grp.txt.gz 2014-03-02 04:14 208 hgFindSpec.sql 2020-12-06 08:09 1.7K hgFindSpec.txt.gz 2020-12-06 08:09 1.1K history.sql 2012-11-06 14:21 1.6K history.txt.gz 2012-11-06 14:21 549 microsat.sql 2015-08-23 20:59 1.5K microsat.txt.gz 2015-08-23 20:59 8.2K mrnaOrientInfo.sql 2018-11-04 07:31 1.8K mrnaOrientInfo.txt.gz 2018-11-04 07:31 644 ncbiRefSeq.sql 2020-05-10 03:28 1.9K ncbiRefSeq.txt.gz 2020-05-10 03:28 1.8M ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K ncbiRefSeqCds.txt.gz 2020-05-10 03:28 155K ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 2.1K ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K ncbiRefSeqLink.txt.gz 2020-05-10 03:28 760K ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75 ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 5.9M ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 1.8M ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 2.2M nestedRepeats.sql 2012-11-06 14:21 1.9K nestedRepeats.txt.gz 2012-11-06 14:21 542K netGalGal6.sql 2019-01-20 20:20 2.1K netGalGal6.txt.gz 2019-01-20 20:20 40M netGeoFor1.sql 2012-11-06 14:21 2.1K netGeoFor1.txt.gz 2012-11-06 14:21 31M netMm10.sql 2012-11-06 14:24 2.1K netMm10.txt.gz 2012-11-06 14:24 7.4M rmsk.sql 2012-11-06 14:21 1.9K rmsk.txt.gz 2012-11-06 14:21 9.3M seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K seqNcbiRefSeq.txt.gz 2020-05-10 03:28 395K simpleRepeat.sql 2012-11-06 14:24 1.9K simpleRepeat.txt.gz 2012-11-06 14:24 3.4M tableDescriptions.sql 2020-04-26 03:23 1.4K tableDescriptions.txt.gz 2020-04-26 03:23 6.1K tableList.sql 2021-05-02 03:12 1.6K tableList.txt.gz 2021-05-02 03:12 2.9K trackDb.sql 2020-12-05 08:57 2.0K trackDb.txt.gz 2020-12-05 08:57 40K ucscToINSDC.sql 2013-09-15 16:01 1.4K ucscToINSDC.txt.gz 2013-09-15 16:01 173K ucscToRefSeq.sql 2018-02-18 07:22 1.4K ucscToRefSeq.txt.gz 2018-02-18 07:22 180K windowmaskerSdust.sql 2012-11-06 14:20 1.5K windowmaskerSdust.txt.gz 2012-11-06 14:20 53M xenoRefFlat.sql 2020-08-19 17:01 1.7K xenoRefFlat.txt.gz 2020-08-19 17:01 25M xenoRefGene.sql 2020-08-19 17:01 1.9K xenoRefGene.txt.gz 2020-08-19 17:01 28M xenoRefSeqAli.sql 2020-08-19 17:01 2.1K xenoRefSeqAli.txt.gz 2020-08-19 17:01 25M