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.
-----------------------------------------------------------------------------
Name Last modified Size Description
Parent Directory -
chainMm10Link.sql 2012-11-06 14:20 1.5K
chainMm10Link.txt.gz 2012-11-06 14:20 42M
gap.sql 2012-11-06 14:20 1.6K
gap.txt.gz 2012-11-06 14:20 622K
gold.sql 2012-11-06 14:20 1.7K
gold.txt.gz 2012-11-06 14:20 1.0M
chromInfo.sql 2012-11-06 14:20 1.4K
chromInfo.txt.gz 2012-11-06 14:20 109K
gc5BaseBw.sql 2012-11-06 14:20 1.3K
gc5BaseBw.txt.gz 2012-11-06 14:20 63
windowmaskerSdust.sql 2012-11-06 14:20 1.5K
windowmaskerSdust.txt.gz 2012-11-06 14:20 53M
genscan.sql 2012-11-06 14:21 1.7K
genscan.txt.gz 2012-11-06 14:21 1.4M
netGeoFor1.sql 2012-11-06 14:21 2.1K
netGeoFor1.txt.gz 2012-11-06 14:21 31M
history.sql 2012-11-06 14:21 1.6K
history.txt.gz 2012-11-06 14:21 549
nestedRepeats.sql 2012-11-06 14:21 1.9K
nestedRepeats.txt.gz 2012-11-06 14:21 542K
rmsk.sql 2012-11-06 14:21 1.9K
rmsk.txt.gz 2012-11-06 14:21 9.3M
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
netMm10.sql 2012-11-06 14:24 2.1K
netMm10.txt.gz 2012-11-06 14:24 7.4M
simpleRepeat.sql 2012-11-06 14:24 1.9K
simpleRepeat.txt.gz 2012-11-06 14:24 3.4M
chainMm10.sql 2012-11-06 14:24 1.7K
chainMm10.txt.gz 2012-11-06 14:24 4.9M
cpgIslandExt.sql 2012-11-06 14:24 1.7K
cpgIslandExt.txt.gz 2012-11-06 14:24 302K
cytoBandIdeo.sql 2013-04-28 18:21 1.5K
cytoBandIdeo.txt.gz 2013-04-28 18:21 113K
ucscToINSDC.sql 2013-09-15 16:01 1.4K
ucscToINSDC.txt.gz 2013-09-15 16:01 173K
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 16:20 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 16:20 335K
augustusGene.sql 2015-07-26 16:22 1.9K
augustusGene.txt.gz 2015-07-26 16:22 1.4M
microsat.sql 2015-08-23 20:59 1.5K
microsat.txt.gz 2015-08-23 20:59 8.2K
ucscToRefSeq.sql 2018-02-18 07:22 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:22 180K
all_mrna.sql 2018-11-04 07:31 2.1K
all_mrna.txt.gz 2018-11-04 07:31 2.5K
mrnaOrientInfo.sql 2018-11-04 07:31 1.8K
mrnaOrientInfo.txt.gz 2018-11-04 07:31 644
chainGalGal6Link.sql 2019-01-20 20:08 1.5K
chainGalGal6Link.txt.gz 2019-01-20 20:10 2.0G
chainGalGal6.sql 2019-01-20 20:18 1.7K
chainGalGal6.txt.gz 2019-01-20 20:18 352M
netGalGal6.sql 2019-01-20 20:20 2.1K
netGalGal6.txt.gz 2019-01-20 20:20 40M
chromAlias.sql 2020-04-12 03:25 1.4K
chromAlias.txt.gz 2020-04-12 03:25 244K
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 90
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
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 395K
xenoRefGene.sql 2020-08-19 17:01 2.0K
xenoRefGene.txt.gz 2020-08-19 17:01 28M
xenoRefFlat.sql 2020-08-19 17:01 1.7K
xenoRefFlat.txt.gz 2020-08-19 17:01 25M
xenoRefSeqAli.sql 2020-08-19 17:01 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 17:01 25M
gbLoaded.sql 2020-08-19 17:01 1.6K
gbLoaded.txt.gz 2020-08-19 17:01 14K
ensGene.sql 2021-05-25 14:36 1.9K
ensGene.txt.gz 2021-05-25 14:36 1.8M
ensGtp.sql 2021-05-25 14:36 1.4K
ensGtp.txt.gz 2021-05-25 14:36 222K
ensemblToGeneName.sql 2021-05-25 14:36 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:36 1.4K
ensemblSource.sql 2021-05-25 14:39 1.4K
ensemblSource.txt.gz 2021-05-25 14:39 70K
ensPep.sql 2021-05-25 14:39 1.3K
ensPep.txt.gz 2021-05-25 14:39 5.0M
trackDb.sql 2023-12-05 13:50 2.1K
trackDb.txt.gz 2023-12-05 13:50 29K
hgFindSpec.sql 2023-12-05 13:50 1.8K
hgFindSpec.txt.gz 2023-12-05 13:50 1.2K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.2K
tableList.sql 2024-11-17 03:37 1.6K
tableList.txt.gz 2024-11-17 03:37 2.9K
bigFiles.sql 2024-11-17 03:37 1.4K
bigFiles.txt.gz 2024-11-17 03:37 94