This directory contains a dump of the UCSC genome annotation database for the
Jun. 2014 (G_variegatus-3.0.2/galVar1) assembly of the malayan flying lemur genome
(galVar1, Washington University (WashU)) .
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/792
http://www.ncbi.nlm.nih.gov/genome/assembly/182621
http://www.ncbi.nlm.nih.gov/bioproject/253111
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=galVar1
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/galVar1/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/galVar1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/galVar1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galVar1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/galVar1/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 galVar1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql galVar1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Malayan flying lemur 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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
augustusGene.sql 2016-08-15 13:07 1.9K
augustusGene.txt.gz 2016-08-15 13:07 3.0M
author.sql 2016-08-15 13:07 1.4K
author.txt.gz 2016-08-15 13:07 2.9M
bigFiles.sql 2024-12-22 03:10 1.4K
bigFiles.txt.gz 2024-12-22 03:10 95
cds.sql 2016-08-15 13:07 1.4K
cds.txt.gz 2016-08-15 13:07 1.7M
cell.sql 2016-08-15 13:07 1.4K
cell.txt.gz 2016-08-15 13:07 40
chainCavPor3.sql 2016-08-15 13:07 1.7K
chainCavPor3.txt.gz 2016-08-15 13:08 655M
chainCavPor3Link.sql 2016-08-15 13:10 1.5K
chainCavPor3Link.txt.gz 2016-08-15 13:14 2.2G
chainHg38.sql 2016-08-15 13:25 1.7K
chainHg38.txt.gz 2016-08-15 13:26 608M
chainHg38Link.sql 2016-08-15 13:28 1.5K
chainHg38Link.txt.gz 2016-08-15 13:31 1.8G
chainMm10.sql 2016-08-15 13:39 1.7K
chainMm10.txt.gz 2016-08-15 13:39 118M
chainMm10Link.sql 2016-08-15 13:39 1.5K
chainMm10Link.txt.gz 2016-08-15 13:40 665M
chainMm39.sql 2020-11-24 09:08 1.7K
chainMm39.txt.gz 2020-11-24 09:08 171M
chainMm39Link.sql 2020-11-24 09:14 1.6K
chainMm39Link.txt.gz 2020-11-24 09:14 777M
chainTupBel1.sql 2016-08-15 13:43 1.7K
chainTupBel1.txt.gz 2016-08-15 13:45 1.3G
chainTupBel1Link.sql 2016-08-15 13:50 1.5K
chainTupBel1Link.txt.gz 2016-08-15 13:55 3.2G
chromAlias.sql 2018-02-18 06:37 1.4K
chromAlias.txt.gz 2018-02-18 06:37 1.7M
chromInfo.sql 2016-08-15 14:09 1.4K
chromInfo.txt.gz 2016-08-15 14:09 534K
cpgIslandExt.sql 2016-08-15 14:09 1.7K
cpgIslandExt.txt.gz 2016-08-15 14:09 1.4M
cpgIslandExtUnmasked.sql 2016-08-15 14:09 1.7K
cpgIslandExtUnmasked.txt.gz 2016-08-15 14:09 1.6M
cytoBandIdeo.sql 2016-08-15 14:09 1.5K
cytoBandIdeo.txt.gz 2016-08-15 14:09 519K
description.sql 2016-08-15 14:09 1.4K
description.txt.gz 2016-08-15 14:09 8.1M
development.sql 2016-08-15 14:09 1.4K
development.txt.gz 2016-08-15 14:09 47
extFile.sql 2016-08-15 14:09 1.4K
extFile.txt.gz 2016-08-15 14:09 80
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 90
gap.sql 2016-08-15 14:09 1.6K
gap.txt.gz 2016-08-15 14:09 3.9M
gbCdnaInfo.sql 2016-08-15 14:09 2.6K
gbCdnaInfo.txt.gz 2016-08-15 14:09 8.8M
gbExtFile.sql 2016-08-15 14:09 1.4K
gbExtFile.txt.gz 2016-08-15 14:09 1.2K
gbLoaded.sql 2020-08-19 10:53 1.6K
gbLoaded.txt.gz 2020-08-19 10:53 41K
gbMiscDiff.sql 2016-08-15 14:09 1.5K
gbMiscDiff.txt.gz 2016-08-15 14:09 4.2K
gbSeq.sql 2016-08-15 14:09 1.7K
gbSeq.txt.gz 2016-08-15 14:09 11M
gbStatus.sql 2016-08-15 14:09 1.9K
gbStatus.txt.gz 2016-08-15 14:09 3.2M
gbWarn.sql 2016-08-15 14:09 1.3K
gbWarn.txt.gz 2016-08-15 14:09 31
gc5BaseBw.sql 2016-08-15 14:09 1.3K
gc5BaseBw.txt.gz 2016-08-15 14:09 66
geneName.sql 2016-08-15 14:09 1.4K
geneName.txt.gz 2016-08-15 14:09 2.2M
genscan.sql 2016-08-15 14:10 1.7K
genscan.txt.gz 2016-08-15 14:10 3.5M
genscanSubopt.sql 2016-08-15 14:10 1.6K
genscanSubopt.txt.gz 2016-08-15 14:10 8.2M
gold.sql 2016-08-15 14:10 1.7K
gold.txt.gz 2016-08-15 14:10 6.2M
grp.sql 2016-08-15 14:10 1.3K
grp.txt.gz 2016-08-15 14:10 213
hgFindSpec.sql 2023-12-05 13:51 1.8K
hgFindSpec.txt.gz 2023-12-05 13:51 1.0K
history.sql 2016-08-15 14:10 1.6K
history.txt.gz 2016-08-15 14:10 1.0K
imageClone.sql 2016-08-15 14:10 1.5K
imageClone.txt.gz 2016-08-15 14:10 35
keyword.sql 2016-08-15 14:10 1.4K
keyword.txt.gz 2016-08-15 14:10 561
library.sql 2016-08-15 14:10 1.4K
library.txt.gz 2016-08-15 14:10 43
microsat.sql 2016-08-15 14:10 1.5K
microsat.txt.gz 2016-08-15 14:10 412K
mrnaClone.sql 2016-08-15 14:10 1.4K
mrnaClone.txt.gz 2016-08-15 14:10 1.3K
multiz5way.sql 2016-08-15 14:10 1.5K
multiz5way.txt.gz 2016-08-15 14:10 142M
multiz5wayFrames.sql 2016-08-15 14:10 1.7K
multiz5wayFrames.txt.gz 2016-08-15 14:10 8.9M
multiz5waySummary.sql 2016-08-15 14:10 1.6K
multiz5waySummary.txt.gz 2016-08-15 14:10 842K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:27 2.3M
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 208K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 328
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.0M
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 6.6M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 2.3M
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.6M
nestedRepeats.sql 2016-08-15 14:11 1.9K
nestedRepeats.txt.gz 2016-08-15 14:11 15M
netCavPor3.sql 2016-08-15 14:11 2.1K
netCavPor3.txt.gz 2016-08-15 14:11 97M
netHg38.sql 2016-08-15 14:11 2.1K
netHg38.txt.gz 2016-08-15 14:11 75M
netMm10.sql 2016-08-15 14:12 2.1K
netMm10.txt.gz 2016-08-15 14:12 85M
netMm39.sql 2020-11-24 09:19 2.1K
netMm39.txt.gz 2020-11-24 09:19 85M
netTupBel1.sql 2016-08-15 14:12 2.1K
netTupBel1.txt.gz 2016-08-15 14:12 79M
organism.sql 2016-08-15 14:13 1.4K
organism.txt.gz 2016-08-15 14:13 264K
phastCons5way.sql 2016-08-15 14:13 1.8K
phastCons5way.txt.gz 2016-08-15 14:13 73M
phastConsElements5way.sql 2016-08-15 14:13 1.6K
phastConsElements5way.txt.gz 2016-08-15 14:13 9.2M
phyloP5way.sql 2016-08-15 14:13 1.8K
phyloP5way.txt.gz 2016-08-15 14:13 75M
productName.sql 2016-08-15 14:14 1.4K
productName.txt.gz 2016-08-15 14:14 2.6M
refLink.sql 2016-08-15 14:14 1.7K
refLink.txt.gz 2016-08-15 14:14 10M
refSeqStatus.sql 2016-08-15 14:14 1.6K
refSeqStatus.txt.gz 2016-08-15 14:14 1.4M
refSeqSummary.sql 2016-08-15 14:14 1.5K
refSeqSummary.txt.gz 2016-08-15 14:14 4.7M
rmsk.sql 2016-08-15 14:14 1.9K
rmsk.txt.gz 2016-08-15 14:14 130M
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 518K
sex.sql 2016-08-15 14:15 1.4K
sex.txt.gz 2016-08-15 14:15 39
simpleRepeat.sql 2016-08-15 14:15 1.9K
simpleRepeat.txt.gz 2016-08-15 14:15 32M
source.sql 2016-08-15 14:15 1.4K
source.txt.gz 2016-08-15 14:15 269K
tableDescriptions.sql 2024-12-21 02:06 1.4K
tableDescriptions.txt.gz 2024-12-21 02:06 8.3K
tableList.sql 2024-12-22 03:10 1.6K
tableList.txt.gz 2024-12-22 03:10 4.3K
tissue.sql 2016-08-15 14:15 1.4K
tissue.txt.gz 2016-08-15 14:15 132
trackDb.sql 2023-12-05 13:51 2.1K
trackDb.txt.gz 2023-12-05 13:51 38K
ucscToINSDC.sql 2016-08-15 14:15 1.4K
ucscToINSDC.txt.gz 2016-08-15 14:15 957K
ucscToRefSeq.sql 2018-02-18 06:37 1.4K
ucscToRefSeq.txt.gz 2018-02-18 06:37 918K
windowmaskerSdust.sql 2016-08-15 14:15 1.5K
windowmaskerSdust.txt.gz 2016-08-15 14:15 165M
xenoRefFlat.sql 2020-08-19 10:53 1.7K
xenoRefFlat.txt.gz 2020-08-19 10:53 38M
xenoRefGene.sql 2020-08-19 10:53 2.0K
xenoRefGene.txt.gz 2020-08-19 10:53 41M
xenoRefSeqAli.sql 2020-08-19 10:53 2.1K
xenoRefSeqAli.txt.gz 2020-08-19 10:53 44M