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