Monkeypox virus
(Photo courtesy of NIAID Integrated Research Facility (IRF))

Common name: monkeypox
Taxonomic name: Monkeypox virus, taxonomy ID: 10244
Sequencing/Assembly provider ID: na
Assembly date: 30 May 2022
Assembly type: na
Assembly level: Complete Genome
Biosample: (n/a)
Assembly accession ID: GCF_014621545.1
Assembly FTP location: GCF/014/621/545/GCF_014621545.1_ASM1462154v1
Total assembly nucleotides: 197,209
Assembly contig count: 1
N50 size: 197,209

Data file downloads

mpxvRivers.fa.gz fasta sequence
mpxvRivers.2bit UCSC 2bit sequence file
mpxvRivers.chromAlias.txt chromAlias file to relate chromosome names
explore the download directory at: hgdownload.soe.ucsc.edu/goldenPath/mpxvRivers/

blat service

There is blat service available for this genome assembly. When viewing this assembly in the genome browser, access the blat service via the Tools -> Blat blue navigation bar menu item.

For local command line blat service, access the blat service via the gfClient command line operation.
See also: hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ to download command line binaries.

To operate this locally, you will need the mpxvRivers.2bit file from:

  https://hgdownload.soe.ucsc.edu/goldenPath/mpxvRivers/

Which can be obtained with rsync via:

  rsync -a -P 
    rsync://hgdownload.soe.ucsc.edu/mpxvRivers/bigZips/mpxvRivers.2bit ./

With that mpxvRivers.2bit file in your working directory where you run this command, for example, a DNA query with your DNA sequence in the file: someDna.fa with result in the file: mpxvRivers.someDna.psl

gfClient -t=dna -q=dna -genome=mpxvRivers -genomeDataDir=mpxvRivers \\ 
    dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa mpxvRivers.someDna.psl

For a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: mpxvRivers.someProtein.psl

gfClient -t=dnax -q=prot -genome=mpxvRivers -genomeDataDir=mpxvRivers \\ 
    dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa mpxvRivers.someProtein.psl

Search the assembly:

By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information. To avoid case sensitivity issues, always use fully lower case gene names.
By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.