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.
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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/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
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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 -
chainTarSyr2Link.txt.gz 2016-02-08 13:58 1.0G
chainHg38Link.txt.gz 2016-02-08 13:52 872M
chainTarSyr2.txt.gz 2016-02-08 13:56 222M
chainHg38.txt.gz 2016-02-08 13:50 198M
windowmaskerSdust.txt.gz 2016-02-08 14:03 136M
rmsk.txt.gz 2016-02-08 14:03 106M
netTarSyr2.txt.gz 2016-02-08 14:02 61M
netHg38.txt.gz 2016-02-08 14:02 47M
xenoRefSeqAli.txt.gz 2020-08-22 06:42 36M
xenoRefGene.txt.gz 2020-08-22 06:42 35M
xenoRefFlat.txt.gz 2020-08-22 06:42 32M
simpleRepeat.txt.gz 2016-02-08 14:03 15M
nestedRepeats.txt.gz 2016-02-08 14:02 12M
ensPep.txt.gz 2018-02-04 08:10 11M
ncbiRefSeqPepTable.txt.gz 2018-02-09 14:19 7.4M
genscanSubopt.txt.gz 2016-02-08 14:02 6.2M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:45 4.8M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:44 3.5M
ncbiRefSeq.txt.gz 2018-02-09 13:44 3.5M
genscan.txt.gz 2016-02-08 14:02 3.2M
ensGene.txt.gz 2018-02-04 08:09 2.8M
augustusGene.txt.gz 2016-02-08 13:50 2.4M
ncbiRefSeqLink.txt.gz 2018-02-09 13:44 1.6M
cpgIslandExtUnmasked.txt.gz 2016-02-08 14:02 1.5M
cpgIslandExt.txt.gz 2016-02-08 14:02 1.4M
seqNcbiRefSeq.txt.gz 2018-02-09 14:19 1.1M
gold.txt.gz 2016-02-08 14:02 868K
gap.txt.gz 2016-02-08 14:02 575K
ensGtp.txt.gz 2018-02-04 08:09 475K
ncbiRefSeqCds.txt.gz 2018-02-09 14:18 383K
microsat.txt.gz 2016-02-08 13:50 297K
ensemblToGeneName.txt.gz 2018-02-04 08:09 228K
ensemblSource.txt.gz 2018-02-04 08:09 131K
chromAlias.txt.gz 2017-09-03 05:39 107K
ucscToRefSeq.txt.gz 2018-02-18 07:23 84K
ucscToINSDC.txt.gz 2016-02-08 14:03 82K
chromInfo.txt.gz 2016-02-08 14:02 61K
cytoBandIdeo.txt.gz 2016-02-08 14:02 57K
trackDb.txt.gz 2023-12-05 13:51 28K
gbLoaded.txt.gz 2020-08-22 06:42 16K
all_mrna.txt.gz 2017-07-09 11:32 9.0K
tableDescriptions.txt.gz 2024-11-23 02:03 6.3K
mrnaOrientInfo.txt.gz 2017-07-09 11:32 3.0K
tableList.txt.gz 2024-11-24 03:14 2.8K
xenoRefSeqAli.sql 2020-08-22 06:42 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:45 2.1K
all_mrna.sql 2017-07-09 11:32 2.1K
netTarSyr2.sql 2016-02-08 14:02 2.1K
netHg38.sql 2016-02-08 14:02 2.1K
trackDb.sql 2023-12-05 13:51 2.1K
ncbiRefSeqLink.sql 2018-02-09 13:44 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:44 2.0K
xenoRefGene.sql 2020-08-22 06:42 2.0K
ncbiRefSeq.sql 2018-02-09 13:44 2.0K
augustusGene.sql 2016-02-08 13:50 1.9K
nestedRepeats.sql 2016-02-08 14:02 1.9K
simpleRepeat.sql 2016-02-08 14:03 1.9K
ensGene.sql 2018-02-04 08:09 1.9K
rmsk.sql 2016-02-08 14:03 1.9K
mrnaOrientInfo.sql 2017-07-09 11:32 1.8K
hgFindSpec.sql 2023-12-05 13:51 1.8K
xenoRefFlat.sql 2020-08-22 06:42 1.7K
cpgIslandExtUnmasked.sql 2016-02-08 14:02 1.7K
chainTarSyr2.sql 2016-02-08 13:56 1.7K
chainHg38.sql 2016-02-08 13:50 1.7K
cpgIslandExt.sql 2016-02-08 14:02 1.7K
genscan.sql 2016-02-08 14:02 1.7K
gold.sql 2016-02-08 14:02 1.7K
gbLoaded.sql 2020-08-22 06:42 1.6K
gap.sql 2016-02-08 14:02 1.6K
history.sql 2016-02-08 14:02 1.6K
seqNcbiRefSeq.sql 2018-02-09 14:19 1.6K
genscanSubopt.sql 2016-02-08 14:02 1.6K
tableList.sql 2024-11-24 03:14 1.6K
chainTarSyr2Link.sql 2016-02-08 13:57 1.5K
chainHg38Link.sql 2016-02-08 13:51 1.5K
cytoBandIdeo.sql 2016-02-08 14:02 1.5K
windowmaskerSdust.sql 2016-02-08 14:03 1.5K
microsat.sql 2016-02-08 13:50 1.5K
extNcbiRefSeq.sql 2018-02-09 14:19 1.5K
ucscToRefSeq.sql 2018-02-18 07:23 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ucscToINSDC.sql 2016-02-08 14:03 1.4K
chromAlias.sql 2017-09-03 05:39 1.4K
ensGtp.sql 2018-02-04 08:09 1.4K
ensemblToGeneName.sql 2018-02-04 08:09 1.4K
chromInfo.sql 2016-02-08 14:02 1.4K
ncbiRefSeqPepTable.sql 2018-02-09 14:19 1.4K
bigFiles.sql 2024-11-24 03:14 1.4K
ncbiRefSeqCds.sql 2018-02-09 14:18 1.4K
ensemblSource.sql 2018-02-04 08:09 1.4K
grp.sql 2016-02-08 14:02 1.3K
ensPep.sql 2018-02-04 08:10 1.3K
ncbiRefSeqOther.sql 2018-02-09 14:18 1.3K
gc5BaseBw.sql 2016-02-08 13:56 1.3K
hgFindSpec.txt.gz 2023-12-05 13:51 1.1K
history.txt.gz 2016-02-08 14:02 511
grp.txt.gz 2016-02-08 14:02 213
bigFiles.txt.gz 2024-11-24 03:14 95
extNcbiRefSeq.txt.gz 2018-02-09 14:19 91
ncbiRefSeqOther.txt.gz 2018-02-09 14:18 75
gc5BaseBw.txt.gz 2016-02-08 13:56 66