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.
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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/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.
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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 -
gbWarn.txt.gz 2016-08-15 14:09 31
imageClone.txt.gz 2016-08-15 14:10 35
sex.txt.gz 2016-08-15 14:15 39
cell.txt.gz 2016-08-15 13:07 40
library.txt.gz 2016-08-15 14:10 43
development.txt.gz 2016-08-15 14:09 47
gc5BaseBw.txt.gz 2016-08-15 14:09 66
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 75
extFile.txt.gz 2016-08-15 14:09 80
extNcbiRefSeq.txt.gz 2020-05-10 03:27 90
bigFiles.txt.gz 2024-04-21 03:14 95
tissue.txt.gz 2016-08-15 14:15 132
grp.txt.gz 2016-08-15 14:10 213
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 328
keyword.txt.gz 2016-08-15 14:10 561
hgFindSpec.txt.gz 2023-12-05 13:51 1.0K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.0K
history.txt.gz 2016-08-15 14:10 1.0K
gbExtFile.txt.gz 2016-08-15 14:09 1.2K
gc5BaseBw.sql 2016-08-15 14:09 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
gbWarn.sql 2016-08-15 14:09 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
mrnaClone.txt.gz 2016-08-15 14:10 1.3K
grp.sql 2016-08-15 14:10 1.3K
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
chromInfo.sql 2016-08-15 14:09 1.4K
cds.sql 2016-08-15 13:07 1.4K
sex.sql 2016-08-15 14:15 1.4K
cell.sql 2016-08-15 13:07 1.4K
author.sql 2016-08-15 13:07 1.4K
source.sql 2016-08-15 14:15 1.4K
tissue.sql 2016-08-15 14:15 1.4K
gbExtFile.sql 2016-08-15 14:09 1.4K
keyword.sql 2016-08-15 14:10 1.4K
library.sql 2016-08-15 14:10 1.4K
bigFiles.sql 2024-04-21 03:14 1.4K
geneName.sql 2016-08-15 14:09 1.4K
organism.sql 2016-08-15 14:13 1.4K
mrnaClone.sql 2016-08-15 14:10 1.4K
description.sql 2016-08-15 14:09 1.4K
development.sql 2016-08-15 14:09 1.4K
productName.sql 2016-08-15 14:14 1.4K
extFile.sql 2016-08-15 14:09 1.4K
chromAlias.sql 2018-02-18 06:37 1.4K
ucscToINSDC.sql 2016-08-15 14:15 1.4K
ucscToRefSeq.sql 2018-02-18 06:37 1.4K
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
tableDescriptions.sql 2024-04-20 02:03 1.5K
gbMiscDiff.sql 2016-08-15 14:09 1.5K
microsat.sql 2016-08-15 14:10 1.5K
refSeqSummary.sql 2016-08-15 14:14 1.5K
imageClone.sql 2016-08-15 14:10 1.5K
windowmaskerSdust.sql 2016-08-15 14:15 1.5K
cytoBandIdeo.sql 2016-08-15 14:09 1.5K
multiz5way.sql 2016-08-15 14:10 1.5K
chainHg38Link.sql 2016-08-15 13:28 1.5K
chainMm10Link.sql 2016-08-15 13:39 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
chainCavPor3Link.sql 2016-08-15 13:10 1.5K
chainTupBel1Link.sql 2016-08-15 13:50 1.5K
chainMm39Link.sql 2020-11-24 09:14 1.6K
phastConsElements5way.sql 2016-08-15 14:13 1.6K
genscanSubopt.sql 2016-08-15 14:10 1.6K
history.sql 2016-08-15 14:10 1.6K
multiz5waySummary.sql 2016-08-15 14:10 1.6K
tableList.sql 2024-04-21 03:14 1.6K
gap.sql 2016-08-15 14:09 1.6K
refSeqStatus.sql 2016-08-15 14:14 1.6K
gbLoaded.sql 2020-08-19 10:53 1.6K
gold.sql 2016-08-15 14:10 1.7K
genscan.sql 2016-08-15 14:10 1.7K
cpgIslandExt.sql 2016-08-15 14:09 1.7K
chainHg38.sql 2016-08-15 13:25 1.7K
chainMm10.sql 2016-08-15 13:39 1.7K
gbSeq.sql 2016-08-15 14:09 1.7K
chainCavPor3.sql 2016-08-15 13:07 1.7K
chainTupBel1.sql 2016-08-15 13:43 1.7K
cpgIslandExtUnmasked.sql 2016-08-15 14:09 1.7K
chainMm39.sql 2020-11-24 09:08 1.7K
multiz5wayFrames.sql 2016-08-15 14:10 1.7K
refLink.sql 2016-08-15 14:14 1.7K
xenoRefFlat.sql 2020-08-19 10:53 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
phyloP5way.sql 2016-08-15 14:13 1.8K
phastCons5way.sql 2016-08-15 14:13 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
rmsk.sql 2016-08-15 14:14 1.9K
gbStatus.sql 2016-08-15 14:09 1.9K
simpleRepeat.sql 2016-08-15 14:15 1.9K
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
nestedRepeats.sql 2016-08-15 14:11 1.9K
augustusGene.sql 2016-08-15 13:07 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
xenoRefGene.sql 2020-08-19 10:53 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
netHg38.sql 2016-08-15 14:11 2.1K
netMm10.sql 2016-08-15 14:12 2.1K
netCavPor3.sql 2016-08-15 14:11 2.1K
netTupBel1.sql 2016-08-15 14:12 2.1K
netMm39.sql 2020-11-24 09:19 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
xenoRefSeqAli.sql 2020-08-19 10:53 2.1K
gbCdnaInfo.sql 2016-08-15 14:09 2.6K
gbMiscDiff.txt.gz 2016-08-15 14:09 4.2K
tableList.txt.gz 2024-04-21 03:14 4.5K
tableDescriptions.txt.gz 2024-04-20 02:03 8.3K
trackDb.txt.gz 2023-12-05 13:51 38K
trackDb_pushedout.txt.gz 2023-12-05 13:51 38K
gbLoaded.txt.gz 2020-08-19 10:53 41K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 208K
organism.txt.gz 2016-08-15 14:13 264K
source.txt.gz 2016-08-15 14:15 269K
microsat.txt.gz 2016-08-15 14:10 412K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 518K
cytoBandIdeo.txt.gz 2016-08-15 14:09 519K
chromInfo.txt.gz 2016-08-15 14:09 534K
multiz5waySummary.txt.gz 2016-08-15 14:10 842K
ucscToRefSeq.txt.gz 2018-02-18 06:37 918K
ucscToINSDC.txt.gz 2016-08-15 14:15 957K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 1.0M
refSeqStatus.txt.gz 2016-08-15 14:14 1.4M
cpgIslandExt.txt.gz 2016-08-15 14:09 1.4M
cpgIslandExtUnmasked.txt.gz 2016-08-15 14:09 1.6M
chromAlias.txt.gz 2018-02-18 06:37 1.7M
cds.txt.gz 2016-08-15 13:07 1.7M
geneName.txt.gz 2016-08-15 14:09 2.2M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 2.3M
ncbiRefSeq.txt.gz 2020-05-10 03:27 2.3M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 2.6M
productName.txt.gz 2016-08-15 14:14 2.6M
author.txt.gz 2016-08-15 13:07 2.9M
augustusGene.txt.gz 2016-08-15 13:07 3.0M
gbStatus.txt.gz 2016-08-15 14:09 3.2M
genscan.txt.gz 2016-08-15 14:10 3.5M
gap.txt.gz 2016-08-15 14:09 3.9M
refSeqSummary.txt.gz 2016-08-15 14:14 4.7M
gold.txt.gz 2016-08-15 14:10 6.2M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 6.6M
description.txt.gz 2016-08-15 14:09 8.1M
genscanSubopt.txt.gz 2016-08-15 14:10 8.2M
gbCdnaInfo.txt.gz 2016-08-15 14:09 8.8M
multiz5wayFrames.txt.gz 2016-08-15 14:10 8.9M
phastConsElements5way.txt.gz 2016-08-15 14:13 9.2M
refLink.txt.gz 2016-08-15 14:14 10M
gbSeq.txt.gz 2016-08-15 14:09 11M
nestedRepeats.txt.gz 2016-08-15 14:11 15M
simpleRepeat.txt.gz 2016-08-15 14:15 32M
xenoRefFlat.txt.gz 2020-08-19 10:53 38M
xenoRefGene.txt.gz 2020-08-19 10:53 41M
xenoRefSeqAli.txt.gz 2020-08-19 10:53 44M
phastCons5way.txt.gz 2016-08-15 14:13 73M
phyloP5way.txt.gz 2016-08-15 14:13 75M
netHg38.txt.gz 2016-08-15 14:11 75M
netTupBel1.txt.gz 2016-08-15 14:12 79M
netMm10.txt.gz 2016-08-15 14:12 85M
netMm39.txt.gz 2020-11-24 09:19 85M
netCavPor3.txt.gz 2016-08-15 14:11 97M
chainMm10.txt.gz 2016-08-15 13:39 118M
rmsk.txt.gz 2016-08-15 14:14 130M
multiz5way.txt.gz 2016-08-15 14:10 142M
windowmaskerSdust.txt.gz 2016-08-15 14:15 165M
chainMm39.txt.gz 2020-11-24 09:08 171M
chainHg38.txt.gz 2016-08-15 13:26 608M
chainCavPor3.txt.gz 2016-08-15 13:08 655M
chainMm10Link.txt.gz 2016-08-15 13:40 665M
chainMm39Link.txt.gz 2020-11-24 09:14 777M
chainTupBel1.txt.gz 2016-08-15 13:45 1.3G
chainHg38Link.txt.gz 2016-08-15 13:31 1.8G
chainCavPor3Link.txt.gz 2016-08-15 13:14 2.2G
chainTupBel1Link.txt.gz 2016-08-15 13:55 3.2G