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 2017-04-07 11:44 1.9K
augustusGene.txt.gz 2017-04-07 11:44 2.2M
author.sql 2017-04-07 11:44 1.4K
author.txt.gz 2017-04-07 11:44 4.2M
bigFiles.sql 2024-11-24 03:06 1.4K
bigFiles.txt.gz 2024-11-24 03:06 69
cds.sql 2017-04-07 11:44 1.4K
cds.txt.gz 2017-04-07 11:44 2.1M
cell.sql 2017-04-07 11:45 1.4K
cell.txt.gz 2017-04-07 11:45 40
chainHg38.sql 2017-04-07 11:45 1.7K
chainHg38.txt.gz 2017-04-07 11:48 315M
chainHg38Link.sql 2017-04-07 11:57 1.5K
chainHg38Link.txt.gz 2017-04-07 12:10 1.0G
chainMm10.sql 2017-04-07 13:06 1.7K
chainMm10.txt.gz 2017-04-07 13:07 70M
chainMm10Link.sql 2017-04-07 13:09 1.5K
chainMm10Link.txt.gz 2017-04-07 13:15 477M
chromAlias.sql 2020-04-12 03:25 1.4K
chromAlias.txt.gz 2020-04-12 03:25 3.0M
chromInfo.sql 2017-04-07 13:38 1.4K
chromInfo.txt.gz 2017-04-07 13:38 1.8M
cpgIslandExt.sql 2017-04-07 13:38 1.7K
cpgIslandExt.txt.gz 2017-04-07 13:38 887K
cpgIslandExtUnmasked.sql 2017-04-07 13:38 1.7K
cpgIslandExtUnmasked.txt.gz 2017-04-07 13:38 1.6M
cytoBandIdeo.sql 2017-04-07 13:38 1.5K
cytoBandIdeo.txt.gz 2017-04-07 13:39 1.9M
description.sql 2017-04-07 13:39 1.4K
description.txt.gz 2017-04-07 13:39 13M
development.sql 2017-04-07 13:39 1.4K
development.txt.gz 2017-04-07 13:39 63
ensGene.sql 2021-05-25 14:19 1.9K
ensGene.txt.gz 2021-05-25 14:19 2.2M
ensGtp.sql 2021-05-25 14:19 1.4K
ensGtp.txt.gz 2021-05-25 14:19 341K
ensPep.sql 2021-05-25 14:21 1.3K
ensPep.txt.gz 2021-05-25 14:21 6.3M
ensemblSource.sql 2021-05-25 14:21 1.4K
ensemblSource.txt.gz 2021-05-25 14:21 96K
ensemblToGeneName.sql 2021-05-25 14:19 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:19 142K
gap.sql 2017-04-07 13:43 1.6K
gap.txt.gz 2017-04-07 13:43 3.9M
gbCdnaInfo.sql 2017-04-07 13:43 2.6K
gbCdnaInfo.txt.gz 2017-04-07 13:43 9.4M
gbExtFile.sql 2017-04-07 13:46 1.4K
gbExtFile.txt.gz 2017-04-07 13:46 11K
gbLoaded.sql 2017-04-07 11:44 1.6K
gbLoaded.txt.gz 2017-04-07 11:44 2.3K
gbMiscDiff.sql 2017-04-07 13:46 1.5K
gbMiscDiff.txt.gz 2017-04-07 13:46 1.5K
gbSeq.sql 2017-04-07 13:46 1.7K
gbSeq.txt.gz 2017-04-07 13:46 13M
gbStatus.sql 2017-04-07 13:47 1.9K
gbStatus.txt.gz 2017-04-07 13:47 3.9M
gbWarn.sql 2017-04-07 11:57 1.3K
gbWarn.txt.gz 2017-04-07 11:57 31
gc5BaseBw.sql 2017-04-07 13:09 1.3K
gc5BaseBw.txt.gz 2017-04-07 13:09 66
geneName.sql 2017-04-07 13:37 1.4K
geneName.txt.gz 2017-04-07 13:37 2.8M
genscan.sql 2017-04-07 13:38 1.7K
genscan.txt.gz 2017-04-07 13:38 3.1M
gold.sql 2017-04-07 13:38 1.7K
gold.txt.gz 2017-04-07 13:38 9.5M
grp.sql 2017-04-07 13:39 1.3K
grp.txt.gz 2017-04-07 13:39 213
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 878
history.sql 2017-04-07 13:43 1.6K
history.txt.gz 2017-04-07 13:43 573
imageClone.sql 2017-04-07 13:46 1.5K
imageClone.txt.gz 2017-04-07 13:46 35
keyword.sql 2017-04-07 11:44 1.4K
keyword.txt.gz 2017-04-07 11:44 750
library.sql 2017-04-07 11:44 1.4K
library.txt.gz 2017-04-07 11:44 43
microsat.sql 2017-04-07 11:45 1.5K
microsat.txt.gz 2017-04-07 11:45 193K
mrnaClone.sql 2017-04-07 11:45 1.4K
mrnaClone.txt.gz 2017-04-07 11:45 1.4K
mrnaOrientInfo.sql 2017-04-07 13:06 1.8K
mrnaOrientInfo.txt.gz 2017-04-07 13:06 84
nestedRepeats.sql 2017-04-07 13:37 1.9K
nestedRepeats.txt.gz 2017-04-07 13:37 14M
netHg38.sql 2017-04-07 13:39 2.1K
netHg38.txt.gz 2017-04-07 13:41 68M
netMm10.sql 2017-04-07 13:43 2.1K
netMm10.txt.gz 2017-04-07 13:45 55M
organism.sql 2017-04-07 13:46 1.4K
organism.txt.gz 2017-04-07 13:46 307K
productName.sql 2017-04-07 13:47 1.4K
productName.txt.gz 2017-04-07 13:47 3.6M
refFlat.sql 2017-04-07 13:38 1.7K
refFlat.txt.gz 2017-04-07 13:38 93
refGene.sql 2017-04-07 13:47 1.9K
refGene.txt.gz 2017-04-07 13:47 106
refLink.sql 2017-04-07 13:47 1.7K
refLink.txt.gz 2017-04-07 13:47 11M
refSeqAli.sql 2017-04-07 13:47 2.1K
refSeqAli.txt.gz 2017-04-07 13:47 103
refSeqStatus.sql 2017-04-07 13:47 1.6K
refSeqStatus.txt.gz 2017-04-07 13:47 1.5M
refSeqSummary.sql 2017-04-07 13:48 1.5K
refSeqSummary.txt.gz 2017-04-07 13:48 5.2M
rmsk.sql 2017-04-07 13:48 1.9K
rmsk.txt.gz 2017-04-07 13:50 148M
sex.sql 2017-04-07 13:55 1.4K
sex.txt.gz 2017-04-07 13:55 39
simpleRepeat.sql 2017-04-07 13:55 1.9K
simpleRepeat.txt.gz 2017-04-07 13:55 13M
source.sql 2017-04-07 13:56 1.4K
source.txt.gz 2017-04-07 13:56 312K
tableDescriptions.sql 2024-11-23 02:03 1.4K
tableDescriptions.txt.gz 2024-11-23 02:03 7.4K
tableList.sql 2024-11-24 03:06 1.6K
tableList.txt.gz 2024-11-24 03:06 3.4K
tissue.sql 2017-04-07 13:56 1.4K
tissue.txt.gz 2017-04-07 13:56 243
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 49K
ucscToINSDC.sql 2017-04-07 13:56 1.4K
ucscToINSDC.txt.gz 2017-04-07 13:56 2.9M
ucscToRefSeq.sql 2017-04-07 13:56 1.4K
ucscToRefSeq.txt.gz 2017-04-07 13:56 900K
windowmaskerSdust.sql 2017-04-07 13:56 1.5K
windowmaskerSdust.txt.gz 2017-04-07 13:57 128M
xenoRefFlat.sql 2017-04-07 14:02 1.7K
xenoRefFlat.txt.gz 2017-04-07 14:02 30M
xenoRefGene.sql 2017-04-07 14:03 1.9K
xenoRefGene.txt.gz 2017-04-07 14:03 33M
xenoRefSeqAli.sql 2017-04-07 14:04 2.1K
xenoRefSeqAli.txt.gz 2017-04-07 14:04 30M