This directory contains a dump of the UCSC genome annotation database for the
Oct. 2014 (Bison_UMD1.0/bisBis1) assembly of the bison genome
(bisBis1, U. Maryland) .
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/8907
http://www.ncbi.nlm.nih.gov/genome/assembly/237421
http://www.ncbi.nlm.nih.gov/bioproject/266339
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=bisBis1
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/bisBis1/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/bisBis1/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/bisBis1/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 bisBis1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql bisBis1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 07-Apr-2017 11:44 1.9K
augustusGene.txt.gz 07-Apr-2017 11:44 2.2M
author.sql 07-Apr-2017 11:44 1.4K
author.txt.gz 07-Apr-2017 11:44 4.2M
bigFiles.sql 09-Jul-2017 07:32 1.4K
bigFiles.txt.gz 09-Jul-2017 07:32 69
cds.sql 07-Apr-2017 11:44 1.4K
cds.txt.gz 07-Apr-2017 11:44 2.1M
cell.sql 07-Apr-2017 11:45 1.4K
cell.txt.gz 07-Apr-2017 11:45 40
chainHg38.sql 07-Apr-2017 11:45 1.7K
chainHg38.txt.gz 07-Apr-2017 11:48 315M
chainHg38Link.sql 07-Apr-2017 11:57 1.5K
chainHg38Link.txt.gz 07-Apr-2017 12:10 1.0G
chainMm10.sql 07-Apr-2017 13:06 1.7K
chainMm10.txt.gz 07-Apr-2017 13:07 70M
chainMm10Link.sql 07-Apr-2017 13:09 1.5K
chainMm10Link.txt.gz 07-Apr-2017 13:15 477M
chromAlias.sql 07-Apr-2017 13:37 1.4K
chromAlias.txt.gz 07-Apr-2017 13:37 2.8M
chromInfo.sql 07-Apr-2017 13:38 1.4K
chromInfo.txt.gz 07-Apr-2017 13:38 1.8M
cpgIslandExt.sql 07-Apr-2017 13:38 1.7K
cpgIslandExt.txt.gz 07-Apr-2017 13:38 887K
cpgIslandExtUnmasked.sql 07-Apr-2017 13:38 1.7K
cpgIslandExtUnmasked.txt.gz 07-Apr-2017 13:38 1.6M
cytoBandIdeo.sql 07-Apr-2017 13:38 1.5K
cytoBandIdeo.txt.gz 07-Apr-2017 13:39 1.9M
description.sql 07-Apr-2017 13:39 1.4K
description.txt.gz 07-Apr-2017 13:39 13M
development.sql 07-Apr-2017 13:39 1.4K
development.txt.gz 07-Apr-2017 13:39 63
gap.sql 07-Apr-2017 13:43 1.6K
gap.txt.gz 07-Apr-2017 13:43 3.9M
gbCdnaInfo.sql 07-Apr-2017 13:43 2.6K
gbCdnaInfo.txt.gz 07-Apr-2017 13:43 9.4M
gbExtFile.sql 07-Apr-2017 13:46 1.4K
gbExtFile.txt.gz 07-Apr-2017 13:46 11K
gbLoaded.sql 07-Apr-2017 11:44 1.6K
gbLoaded.txt.gz 07-Apr-2017 11:44 2.3K
gbMiscDiff.sql 07-Apr-2017 13:46 1.5K
gbMiscDiff.txt.gz 07-Apr-2017 13:46 1.5K
gbSeq.sql 07-Apr-2017 13:46 1.7K
gbSeq.txt.gz 07-Apr-2017 13:46 13M
gbStatus.sql 07-Apr-2017 13:47 1.9K
gbStatus.txt.gz 07-Apr-2017 13:47 3.9M
gbWarn.sql 07-Apr-2017 11:57 1.3K
gbWarn.txt.gz 07-Apr-2017 11:57 31
gc5BaseBw.sql 07-Apr-2017 13:09 1.3K
gc5BaseBw.txt.gz 07-Apr-2017 13:09 66
geneName.sql 07-Apr-2017 13:37 1.4K
geneName.txt.gz 07-Apr-2017 13:37 2.8M
genscan.sql 07-Apr-2017 13:38 1.7K
genscan.txt.gz 07-Apr-2017 13:38 3.1M
gold.sql 07-Apr-2017 13:38 1.7K
gold.txt.gz 07-Apr-2017 13:38 9.5M
grp.sql 07-Apr-2017 13:39 1.3K
grp.txt.gz 07-Apr-2017 13:39 213
hgFindSpec.sql 09-Jul-2017 07:32 1.7K
hgFindSpec.txt.gz 09-Jul-2017 07:32 536
history.sql 07-Apr-2017 13:43 1.6K
history.txt.gz 07-Apr-2017 13:43 573
imageClone.sql 07-Apr-2017 13:46 1.5K
imageClone.txt.gz 07-Apr-2017 13:46 35
keyword.sql 07-Apr-2017 11:44 1.4K
keyword.txt.gz 07-Apr-2017 11:44 750
library.sql 07-Apr-2017 11:44 1.4K
library.txt.gz 07-Apr-2017 11:44 43
microsat.sql 07-Apr-2017 11:45 1.5K
microsat.txt.gz 07-Apr-2017 11:45 193K
mrnaClone.sql 07-Apr-2017 11:45 1.4K
mrnaClone.txt.gz 07-Apr-2017 11:45 1.4K
mrnaOrientInfo.sql 07-Apr-2017 13:06 1.8K
mrnaOrientInfo.txt.gz 07-Apr-2017 13:06 84
nestedRepeats.sql 07-Apr-2017 13:37 1.9K
nestedRepeats.txt.gz 07-Apr-2017 13:37 14M
netHg38.sql 07-Apr-2017 13:39 2.1K
netHg38.txt.gz 07-Apr-2017 13:41 68M
netMm10.sql 07-Apr-2017 13:43 2.1K
netMm10.txt.gz 07-Apr-2017 13:45 55M
organism.sql 07-Apr-2017 13:46 1.4K
organism.txt.gz 07-Apr-2017 13:46 307K
productName.sql 07-Apr-2017 13:47 1.4K
productName.txt.gz 07-Apr-2017 13:47 3.6M
refFlat.sql 07-Apr-2017 13:38 1.7K
refFlat.txt.gz 07-Apr-2017 13:38 93
refGene.sql 07-Apr-2017 13:47 1.9K
refGene.txt.gz 07-Apr-2017 13:47 106
refLink.sql 07-Apr-2017 13:47 1.7K
refLink.txt.gz 07-Apr-2017 13:47 11M
refSeqAli.sql 07-Apr-2017 13:47 2.1K
refSeqAli.txt.gz 07-Apr-2017 13:47 103
refSeqStatus.sql 07-Apr-2017 13:47 1.6K
refSeqStatus.txt.gz 07-Apr-2017 13:47 1.5M
refSeqSummary.sql 07-Apr-2017 13:48 1.5K
refSeqSummary.txt.gz 07-Apr-2017 13:48 5.2M
rmsk.sql 07-Apr-2017 13:48 1.9K
rmsk.txt.gz 07-Apr-2017 13:50 148M
sex.sql 07-Apr-2017 13:55 1.4K
sex.txt.gz 07-Apr-2017 13:55 39
simpleRepeat.sql 07-Apr-2017 13:55 1.9K
simpleRepeat.txt.gz 07-Apr-2017 13:55 13M
source.sql 07-Apr-2017 13:56 1.4K
source.txt.gz 07-Apr-2017 13:56 312K
tableDescriptions.sql 09-Jul-2017 07:32 1.4K
tableDescriptions.txt.gz 09-Jul-2017 07:32 6.0K
tableList.sql 09-Jul-2017 07:32 1.5K
tableList.txt.gz 09-Jul-2017 07:32 3.2K
tissue.sql 07-Apr-2017 13:56 1.4K
tissue.txt.gz 07-Apr-2017 13:56 243
trackDb.sql 09-Jul-2017 07:32 2.0K
trackDb.txt.gz 09-Jul-2017 07:32 17K
ucscToINSDC.sql 07-Apr-2017 13:56 1.4K
ucscToINSDC.txt.gz 07-Apr-2017 13:56 2.9M
ucscToRefSeq.sql 07-Apr-2017 13:56 1.4K
ucscToRefSeq.txt.gz 07-Apr-2017 13:56 900K
windowmaskerSdust.sql 07-Apr-2017 13:56 1.5K
windowmaskerSdust.txt.gz 07-Apr-2017 13:57 128M
xenoRefFlat.sql 07-Apr-2017 14:02 1.7K
xenoRefFlat.txt.gz 07-Apr-2017 14:02 30M
xenoRefGene.sql 07-Apr-2017 14:03 1.9K
xenoRefGene.txt.gz 07-Apr-2017 14:03 33M
xenoRefSeqAli.sql 07-Apr-2017 14:04 2.1K
xenoRefSeqAli.txt.gz 07-Apr-2017 14:04 30M