This directory contains a dump of the UCSC genome annotation database for the
May 2015 (Mouse lemur/micMur2) assembly of the mouse lemur genome
(micMur2, Broad Institute and Baylor College of Medicine Mmur_2.0) .
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/777
http://www.ncbi.nlm.nih.gov/genome/assembly/329621
http://www.ncbi.nlm.nih.gov/bioproject/19967
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=micMur2
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/micMur2/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/micMur2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/micMur2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/micMur2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/micMur2/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 micMur2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql micMur2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Mouse lemur genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
-----------------------------------------------------------------------------
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 -
augustusGene.sql 2016-02-08 13:50 1.9K
augustusGene.txt.gz 2016-02-08 13:50 2.4M
chainHg38.sql 2016-02-08 13:50 1.7K
microsat.sql 2016-02-08 13:50 1.5K
microsat.txt.gz 2016-02-08 13:50 297K
chainHg38.txt.gz 2016-02-08 13:50 198M
chainHg38Link.sql 2016-02-08 13:51 1.5K
chainHg38Link.txt.gz 2016-02-08 13:52 872M
chainTarSyr2.sql 2016-02-08 13:56 1.7K
gc5BaseBw.sql 2016-02-08 13:56 1.3K
gc5BaseBw.txt.gz 2016-02-08 13:56 66
chainTarSyr2.txt.gz 2016-02-08 13:56 222M
chainTarSyr2Link.sql 2016-02-08 13:57 1.5K
chainTarSyr2Link.txt.gz 2016-02-08 13:58 1.0G
genscan.sql 2016-02-08 14:02 1.7K
genscan.txt.gz 2016-02-08 14:02 3.2M
chromInfo.sql 2016-02-08 14:02 1.4K
chromInfo.txt.gz 2016-02-08 14:02 61K
cpgIslandExt.sql 2016-02-08 14:02 1.7K
cpgIslandExt.txt.gz 2016-02-08 14:02 1.4M
genscanSubopt.sql 2016-02-08 14:02 1.6K
genscanSubopt.txt.gz 2016-02-08 14:02 6.2M
cpgIslandExtUnmasked.sql 2016-02-08 14:02 1.7K
cpgIslandExtUnmasked.txt.gz 2016-02-08 14:02 1.5M
cytoBandIdeo.sql 2016-02-08 14:02 1.5K
cytoBandIdeo.txt.gz 2016-02-08 14:02 57K
gold.sql 2016-02-08 14:02 1.7K
gold.txt.gz 2016-02-08 14:02 868K
grp.sql 2016-02-08 14:02 1.3K
grp.txt.gz 2016-02-08 14:02 213
nestedRepeats.sql 2016-02-08 14:02 1.9K
nestedRepeats.txt.gz 2016-02-08 14:02 12M
gap.sql 2016-02-08 14:02 1.6K
gap.txt.gz 2016-02-08 14:02 575K
history.sql 2016-02-08 14:02 1.6K
history.txt.gz 2016-02-08 14:02 511
netHg38.sql 2016-02-08 14:02 2.1K
netHg38.txt.gz 2016-02-08 14:02 47M
netTarSyr2.sql 2016-02-08 14:02 2.1K
netTarSyr2.txt.gz 2016-02-08 14:02 61M
rmsk.sql 2016-02-08 14:03 1.9K
rmsk.txt.gz 2016-02-08 14:03 106M
simpleRepeat.sql 2016-02-08 14:03 1.9K
simpleRepeat.txt.gz 2016-02-08 14:03 15M
ucscToINSDC.sql 2016-02-08 14:03 1.4K
ucscToINSDC.txt.gz 2016-02-08 14:03 82K
windowmaskerSdust.sql 2016-02-08 14:03 1.5K
windowmaskerSdust.txt.gz 2016-02-08 14:03 136M
all_mrna.sql 2017-07-09 11:32 2.1K
all_mrna.txt.gz 2017-07-09 11:32 9.0K
mrnaOrientInfo.sql 2017-07-09 11:32 1.8K
mrnaOrientInfo.txt.gz 2017-07-09 11:32 3.0K
chromAlias.sql 2017-09-03 05:39 1.4K
chromAlias.txt.gz 2017-09-03 05:39 107K
ensGene.sql 2018-02-04 08:09 1.9K
ensGene.txt.gz 2018-02-04 08:09 2.8M
ensGtp.sql 2018-02-04 08:09 1.4K
ensGtp.txt.gz 2018-02-04 08:09 475K
ensemblSource.sql 2018-02-04 08:09 1.4K
ensemblSource.txt.gz 2018-02-04 08:09 131K
ensemblToGeneName.sql 2018-02-04 08:09 1.4K
ensemblToGeneName.txt.gz 2018-02-04 08:09 228K
ensPep.sql 2018-02-04 08:10 1.3K
ensPep.txt.gz 2018-02-04 08:10 11M
ncbiRefSeq.sql 2018-02-09 13:44 2.0K
ncbiRefSeq.txt.gz 2018-02-09 13:44 3.5M
ncbiRefSeqPredicted.sql 2018-02-09 13:44 2.0K
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:44 3.5M
ncbiRefSeqLink.sql 2018-02-09 13:44 2.0K
ncbiRefSeqLink.txt.gz 2018-02-09 13:44 1.6M
ncbiRefSeqPsl.sql 2018-02-09 13:45 2.1K
ncbiRefSeqPsl.txt.gz 2018-02-09 13:45 4.8M
ncbiRefSeqOther.sql 2018-02-09 14:18 1.3K
ncbiRefSeqOther.txt.gz 2018-02-09 14:18 75
ncbiRefSeqCds.sql 2018-02-09 14:18 1.4K
ncbiRefSeqCds.txt.gz 2018-02-09 14:18 383K
ncbiRefSeqPepTable.sql 2018-02-09 14:19 1.4K
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:19 7.4M
extNcbiRefSeq.sql 2018-02-09 14:19 1.5K
extNcbiRefSeq.txt.gz 2018-02-09 14:19 91
seqNcbiRefSeq.sql 2018-02-09 14:19 1.6K
seqNcbiRefSeq.txt.gz 2018-02-09 14:19 1.1M
ucscToRefSeq.sql 2018-02-18 07:23 1.4K
ucscToRefSeq.txt.gz 2018-02-18 07:23 84K
xenoRefGene.sql 2020-08-22 06:42 2.0K
xenoRefGene.txt.gz 2020-08-22 06:42 35M
xenoRefFlat.sql 2020-08-22 06:42 1.7K
xenoRefFlat.txt.gz 2020-08-22 06:42 32M
xenoRefSeqAli.sql 2020-08-22 06:42 2.1K
xenoRefSeqAli.txt.gz 2020-08-22 06:42 36M
gbLoaded.sql 2020-08-22 06:42 1.6K
gbLoaded.txt.gz 2020-08-22 06:42 16K
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 28K
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.1K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
tableList.sql 2024-11-17 03:23 1.6K
tableList.txt.gz 2024-11-17 03:23 2.8K
bigFiles.sql 2024-11-17 03:23 1.4K
bigFiles.txt.gz 2024-11-17 03:23 95