This directory contains a dump of the UCSC genome annotation database for
the Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) assembly of the microbat genome (myoLuc2, Broad Institute (NCBI Project ID: 16951, Accession: GCA_000147115.1)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by Broad Institute of MIT and Harvard.
For more information on the microbat genome, see the project website:
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=16951
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=myoLuc2
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/myoLuc2/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/myoLuc2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/myoLuc2/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 myoLuc2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql myoLuc2 --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.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-19 19:52 37M
xenoRefSeqAli.sql 2020-08-19 19:52 2.1K
xenoRefGene.txt.gz 2020-08-19 19:39 37M
xenoRefGene.sql 2020-08-19 19:39 2.0K
xenoRefFlat.txt.gz 2020-08-19 19:52 33M
xenoRefFlat.sql 2020-08-19 19:52 1.7K
xenoMrna.txt.gz 2020-08-19 19:23 370M
xenoMrna.sql 2020-08-19 19:23 2.1K
ucscToRefSeq.txt.gz 2018-02-18 07:37 88K
ucscToRefSeq.sql 2018-02-18 07:37 1.4K
ucscToINSDC.txt.gz 2013-09-15 16:53 85K
ucscToINSDC.sql 2013-09-15 16:53 1.4K
trackDb.txt.gz 2023-12-05 13:53 28K
trackDb.sql 2023-12-05 13:53 2.1K
tableDescriptions.txt.gz 2024-11-16 02:03 6.1K
tableDescriptions.sql 2024-11-16 02:03 1.5K
simpleRepeat.txt.gz 2011-11-02 16:39 17M
simpleRepeat.sql 2011-11-02 16:39 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 763K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
rmsk.txt.gz 2011-11-02 16:45 83M
rmsk.sql 2011-11-02 16:44 1.8K
netMm10.txt.gz 2013-10-27 18:54 50M
netMm10.sql 2013-10-27 18:54 2.1K
nestedRepeats.txt.gz 2011-11-02 16:48 8.5M
nestedRepeats.sql 2011-11-02 16:47 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.5M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.6M
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.4M
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 968
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 291K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.8M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
mrnaOrientInfo.txt.gz 2017-09-18 10:08 653
mrnaOrientInfo.sql 2017-09-18 10:08 1.8K
microsat.txt.gz 2015-08-23 22:06 778K
microsat.sql 2015-08-23 22:06 1.5K
history.txt.gz 2011-11-02 16:42 340
history.sql 2011-11-02 16:42 1.5K
hgFindSpec.txt.gz 2023-12-05 13:53 1.3K
hgFindSpec.sql 2023-12-05 13:53 1.8K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.3K
gold.txt.gz 2011-11-02 16:39 1.1M
gold.sql 2011-11-02 16:39 1.6K
genscan.txt.gz 2013-12-10 02:57 3.4M
genscan.sql 2013-12-10 02:57 1.7K
gc5BaseBw.txt.gz 2011-11-02 16:42 63
gc5BaseBw.sql 2011-11-02 16:42 1.2K
gbLoaded.txt.gz 2020-08-19 19:54 9.1K
gbLoaded.sql 2020-08-19 19:54 1.6K
gap.txt.gz 2011-11-02 16:38 798K
gap.sql 2011-11-02 16:38 1.5K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:38 113K
ensemblToGeneName.sql 2021-05-25 14:38 1.4K
ensemblSource.txt.gz 2021-05-25 14:41 83K
ensemblSource.sql 2021-05-25 14:41 1.4K
ensPep.txt.gz 2021-05-25 14:41 6.0M
ensPep.sql 2021-05-25 14:41 1.3K
ensGtp.txt.gz 2021-05-25 14:38 276K
ensGtp.sql 2021-05-25 14:38 1.4K
ensGene.txt.gz 2021-05-25 14:38 2.0M
ensGene.sql 2021-05-25 14:38 1.9K
cytoBandIdeo.txt.gz 2013-04-28 19:14 57K
cytoBandIdeo.sql 2013-04-28 19:14 1.5K
cpgIslandExtUnmasked.txt.gz 2014-06-01 17:11 1.2M
cpgIslandExtUnmasked.sql 2014-06-01 17:11 1.7K
cpgIslandExt.txt.gz 2011-11-02 16:39 1.1M
cpgIslandExt.sql 2011-11-02 16:39 1.6K
chromInfo.txt.gz 2011-11-02 16:39 60K
chromInfo.sql 2011-11-02 16:39 1.3K
chromAlias.txt.gz 2018-02-18 07:37 171K
chromAlias.sql 2018-02-18 07:37 1.4K
chainMm10Link.txt.gz 2013-10-27 18:53 420M
chainMm10Link.sql 2013-10-27 18:52 1.5K
chainMm10.txt.gz 2013-10-27 18:52 63M
chainMm10.sql 2013-10-27 18:52 1.7K
blastHg18KG.txt.gz 2011-11-02 16:50 3.5M
blastHg18KG.sql 2011-11-02 16:50 2.1K
augustusGene.txt.gz 2015-07-26 16:56 2.4M
augustusGene.sql 2015-07-26 16:56 1.9K
all_mrna.txt.gz 2017-09-18 10:08 2.4K
all_mrna.sql 2017-09-18 10:08 2.1K