This directory contains a dump of the UCSC genome annotation database for the
Sierra Leone 2014 (G3683/KM034562.1/eboVir3) assembly of the
Ebola virus 2014 genome
(eboVir3, West Africa 01 June 2014 EBOV/G3683/KM034562.1) .
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/4887
http://www.ncbi.nlm.nih.gov/genome/assembly/KM034561
http://www.ncbi.nlm.nih.gov/bioproject/257197
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=eboVir3
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/eboVir3/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/eboVir3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/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 eboVir3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql eboVir3 --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 -
chromInfo.sql 2014-09-30 15:38 1.4K
chromInfo.txt.gz 2014-09-30 15:38 71
cytoBandIdeo.sql 2014-09-30 15:38 1.5K
cytoBandIdeo.txt.gz 2014-09-30 15:38 186
gap.sql 2014-09-30 15:38 1.6K
gap.txt.gz 2014-09-30 15:38 28
gireZebovMissense.sql 2014-09-30 15:38 1.3K
gireZebovMissense.txt.gz 2014-09-30 15:38 81
gold.sql 2014-09-30 15:38 1.7K
gold.txt.gz 2014-09-30 15:38 61
ncbiGene.sql 2014-09-30 15:38 1.7K
ncbiGene.txt.gz 2014-09-30 15:38 238
ncbiGenePfam.sql 2014-09-30 15:38 1.8K
ncbiGenePfam.txt.gz 2014-09-30 15:38 493
pdb.sql 2014-09-30 15:38 1.8K
pdb.txt.gz 2014-09-30 15:38 880
gc5BaseBw.sql 2014-09-30 15:38 1.3K
gc5BaseBw.txt.gz 2014-09-30 15:38 66
geneDesc.sql 2014-09-30 15:38 1.3K
geneDesc.txt.gz 2014-09-30 15:38 2.9K
gire2014.sql 2014-09-30 15:38 1.3K
gire2014.txt.gz 2014-09-30 15:38 64
gire2014FixedMissense.sql 2014-09-30 15:38 1.3K
gire2014FixedMissense.txt.gz 2014-09-30 15:38 86
gire2014KikwitMissense.sql 2014-09-30 15:38 1.3K
gire2014KikwitMissense.txt.gz 2014-09-30 15:38 88
gire2014MayingaMissense.sql 2014-09-30 15:38 1.3K
gire2014MayingaMissense.txt.gz 2014-09-30 15:38 90
gire2014Missense.sql 2014-09-30 15:38 1.3K
gire2014Missense.txt.gz 2014-09-30 15:38 80
gire2014PolymorphicMissense.sql 2014-09-30 15:38 1.3K
gire2014PolymorphicMissense.txt.gz 2014-09-30 15:38 98
gire2014SpecificSnps.sql 2014-09-30 15:38 1.3K
gire2014SpecificSnps.txt.gz 2014-09-30 15:38 84
gireIntraHost.sql 2014-09-30 15:38 1.3K
gireIntraHost.txt.gz 2014-09-30 15:38 74
gireZebov.sql 2014-09-30 15:38 1.3K
gireZebov.txt.gz 2014-09-30 15:38 65
grp.sql 2014-09-30 15:38 1.3K
grp.txt.gz 2014-09-30 15:38 221
history.sql 2014-09-30 15:38 1.6K
history.txt.gz 2014-09-30 15:38 682
mafSnp160way.sql 2014-09-30 15:38 1.5K
mafSnp160way.txt.gz 2014-09-30 15:38 602K
mafSnpStrainName160way.sql 2014-09-30 15:38 1.6K
mafSnpStrainName160way.txt.gz 2014-09-30 15:38 675K
multiz160way.sql 2014-09-30 15:38 1.5K
multiz160way.txt.gz 2014-09-30 15:38 2.2K
multiz160wayFrames.sql 2014-09-30 15:38 1.7K
multiz160wayFrames.txt.gz 2014-09-30 15:38 176
strainName160way.sql 2014-09-30 15:38 1.5K
strainName160way.txt.gz 2014-09-30 15:38 2.2K
strainName160wayFrames.sql 2014-09-30 15:38 1.8K
strainName160wayFrames.txt.gz 2014-09-30 15:38 180
iedbBcell.sql 2014-10-19 10:44 1.3K
iedbBcell.txt.gz 2014-10-19 10:44 69
iedbBcellNeg.sql 2014-10-19 10:44 1.3K
iedbBcellNeg.txt.gz 2014-10-19 10:44 75
iedbTcellI.sql 2014-10-19 10:44 1.3K
iedbTcellI.txt.gz 2014-10-19 10:44 71
iedbTcellII.sql 2014-10-19 10:44 1.3K
iedbTcellII.txt.gz 2014-10-19 10:44 73
spAnnot.sql 2014-10-19 10:44 1.3K
spAnnot.txt.gz 2014-10-19 10:44 61
spMut.sql 2014-10-19 10:44 1.3K
spMut.txt.gz 2014-10-19 10:44 57
spStruct.sql 2014-10-19 10:44 1.3K
spStruct.txt.gz 2014-10-19 10:44 63
muPIT.sql 2014-11-02 20:43 1.5K
muPIT.txt.gz 2014-11-02 20:43 6.7K
phastCons160way.sql 2014-11-02 20:43 1.8K
phastCons160way.txt.gz 2014-11-02 20:43 567
phastConsElements160way.sql 2014-11-02 20:43 1.6K
phastConsElements160way.txt.gz 2014-11-02 20:43 1.4K
phyloP160way.sql 2014-11-02 20:43 1.8K
phyloP160way.txt.gz 2014-11-02 20:43 685
strainPhastCons160way.sql 2014-11-02 20:43 1.8K
strainPhastCons160way.txt.gz 2014-11-02 20:43 573
strainPhastConsElements160way.sql 2014-11-02 20:43 1.6K
strainPhastConsElements160way.txt.gz 2014-11-02 20:43 1.4K
strainPhyloP160way.sql 2014-11-02 20:43 1.8K
strainPhyloP160way.txt.gz 2014-11-02 20:43 691
iedbSupp3.sql 2014-12-21 20:39 1.3K
iedbSupp3.txt.gz 2014-12-21 20:39 70
iedbsupp1A0101.sql 2014-12-21 20:39 1.3K
iedbsupp1A0101.txt.gz 2014-12-21 20:39 80
iedbsupp1A0201.sql 2014-12-21 20:39 1.3K
iedbsupp1A0201.txt.gz 2014-12-21 20:39 80
iedbsupp1A0203.sql 2014-12-21 20:39 1.3K
iedbsupp1A0203.txt.gz 2014-12-21 20:39 80
iedbsupp1A0206.sql 2014-12-21 20:39 1.3K
iedbsupp1A0206.txt.gz 2014-12-21 20:39 80
iedbsupp1A0301.sql 2014-12-21 20:39 1.3K
iedbsupp1A0301.txt.gz 2014-12-21 20:39 80
iedbsupp1B0702.sql 2014-12-21 20:39 1.3K
iedbsupp1B0702.txt.gz 2014-12-21 20:39 80
iedbsupp1B0801.sql 2014-12-21 20:39 1.3K
iedbsupp1B0801.txt.gz 2014-12-21 20:39 80
iedbsupp1B1501.sql 2014-12-21 20:39 1.3K
iedbsupp1B1501.txt.gz 2014-12-21 20:39 80
iedbsupp1B3501.sql 2014-12-21 20:39 1.3K
iedbsupp1B3501.txt.gz 2014-12-21 20:39 80
iedbsupp1B4001.sql 2014-12-21 20:39 1.3K
iedbsupp1B4001.txt.gz 2014-12-21 20:39 80
iedbsupp1B4402.sql 2014-12-21 20:39 1.3K
iedbsupp1B4402.txt.gz 2014-12-21 20:39 80
iedbsupp1B4403.sql 2014-12-21 20:39 1.3K
iedbsupp1B4403.txt.gz 2014-12-21 20:39 80
iedbsupp2A20102.sql 2014-12-21 20:39 1.3K
iedbsupp2A20102.txt.gz 2014-12-21 20:39 82
iedbsupp1A1101.sql 2014-12-21 20:39 1.3K
iedbsupp1A1101.txt.gz 2014-12-21 20:39 80
iedbsupp1A2301.sql 2014-12-21 20:39 1.3K
iedbsupp1A2301.txt.gz 2014-12-21 20:39 80
iedbsupp1A2402.sql 2014-12-21 20:39 1.3K
iedbsupp1A2402.txt.gz 2014-12-21 20:39 80
iedbsupp1A2601.sql 2014-12-21 20:39 1.3K
iedbsupp1A2601.txt.gz 2014-12-21 20:39 80
iedbsupp1A3001.sql 2014-12-21 20:39 1.3K
iedbsupp1A3001.txt.gz 2014-12-21 20:39 80
iedbsupp1A3002.sql 2014-12-21 20:39 1.3K
iedbsupp1A3002.txt.gz 2014-12-21 20:39 80
iedbsupp1A3101.sql 2014-12-21 20:39 1.3K
iedbsupp1A3101.txt.gz 2014-12-21 20:39 80
iedbsupp1A3201.sql 2014-12-21 20:39 1.3K
iedbsupp1A3201.txt.gz 2014-12-21 20:39 80
iedbsupp1A3301.sql 2014-12-21 20:39 1.3K
iedbsupp1A3301.txt.gz 2014-12-21 20:39 80
iedbsupp1A6801.sql 2014-12-21 20:39 1.3K
iedbsupp1A6801.txt.gz 2014-12-21 20:39 80
iedbsupp1A6802.sql 2014-12-21 20:39 1.3K
iedbsupp1A6802.txt.gz 2014-12-21 20:39 80
iedbsupp1B5101.sql 2014-12-21 20:39 1.3K
iedbsupp1B5101.txt.gz 2014-12-21 20:39 80
iedbsupp1B5301.sql 2014-12-21 20:39 1.3K
iedbsupp1B5301.txt.gz 2014-12-21 20:39 80
iedbsupp1B5701.sql 2014-12-21 20:39 1.3K
iedbsupp1B5701.txt.gz 2014-12-21 20:39 80
iedbsupp1B5801.sql 2014-12-21 20:39 1.3K
iedbsupp1B5801.txt.gz 2014-12-21 20:39 80
iedbsupp2A01.sql 2014-12-21 20:39 1.3K
iedbsupp2A01.txt.gz 2014-12-21 20:39 76
iedbsupp2A02.sql 2014-12-21 20:39 1.3K
iedbsupp2A02.txt.gz 2014-12-21 20:39 76
iedbsupp2A07.sql 2014-12-21 20:39 1.3K
iedbsupp2A07.txt.gz 2014-12-21 20:39 76
iedbsupp2A11.sql 2014-12-21 20:39 1.3K
iedbsupp2A11.txt.gz 2014-12-21 20:39 76
iedbsupp2A70103.sql 2014-12-21 20:39 1.3K
iedbsupp2A70103.txt.gz 2014-12-21 20:39 82
iedbsupp2A102201.sql 2014-12-21 20:39 1.3K
iedbsupp2A102201.txt.gz 2014-12-21 20:39 84
iedbsupp2A102601.sql 2014-12-21 20:39 1.3K
iedbsupp2A102601.txt.gz 2014-12-21 20:39 84
iedbsupp2B00101.sql 2014-12-21 20:39 1.3K
iedbsupp2B00101.txt.gz 2014-12-21 20:39 82
iedbsupp2B00301.sql 2014-12-21 20:39 1.3K
iedbsupp2B00301.txt.gz 2014-12-21 20:39 82
iedbsupp2B01.sql 2014-12-21 20:39 1.3K
iedbsupp2B01.txt.gz 2014-12-21 20:39 76
iedbsupp2B01001.sql 2014-12-21 20:39 1.3K
iedbsupp2B01001.txt.gz 2014-12-21 20:39 82
iedbsupp2B03901.sql 2014-12-21 20:39 1.3K
iedbsupp2B03901.txt.gz 2014-12-21 20:39 82
iedbsupp2B06601.sql 2014-12-21 20:39 1.3K
iedbsupp2B06601.txt.gz 2014-12-21 20:39 82
iedbsupp2B08.sql 2014-12-21 20:39 1.3K
iedbsupp2B08.txt.gz 2014-12-21 20:39 76
iedbsupp2B08301.sql 2014-12-21 20:39 1.3K
iedbsupp2B08301.txt.gz 2014-12-21 20:39 82
iedbsupp2B08701.sql 2014-12-21 20:39 1.3K
iedbsupp2B08701.txt.gz 2014-12-21 20:39 82
iedbsupp2B09001.sql 2014-12-21 20:39 1.3K
iedbsupp2B09001.txt.gz 2014-12-21 20:39 82
iedbsupp2B17.sql 2014-12-21 20:39 1.3K
iedbsupp2B17.txt.gz 2014-12-21 20:39 76
newSequences.sql 2015-02-24 15:04 1.5K
newSequences.txt.gz 2015-02-24 15:04 169
newSequencesFrames.sql 2015-02-24 15:04 1.7K
newSequencesFrames.txt.gz 2015-02-24 15:04 3.8K
newSequencesSnpView.sql 2015-02-24 15:04 1.6K
newSequencesSnpView.txt.gz 2015-02-24 15:04 47K
patBulk.sql 2016-04-10 03:26 1.3K
patBulk.txt.gz 2016-04-10 03:26 61
patNonBulk.sql 2016-04-10 03:26 1.3K
patNonBulk.txt.gz 2016-04-10 03:26 67
extFile.sql 2017-01-01 13:06 1.4K
extFile.txt.gz 2017-01-01 13:06 347
trackDb.sql 2023-03-28 13:48 2.1K
trackDb.txt.gz 2023-03-28 13:48 37K
hgFindSpec.sql 2023-03-28 13:48 1.8K
hgFindSpec.txt.gz 2023-03-28 13:48 255
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 3.4K
tableList.sql 2024-11-24 03:30 1.6K
tableList.txt.gz 2024-11-24 03:30 1.9K
bigFiles.sql 2024-11-24 03:30 1.4K
bigFiles.txt.gz 2024-11-24 03:30 590