Share this genome browser with the link: https://http_host/h/GCA_050655635.1
Common name: rust fungi
Taxonomic name: Puccinia silphii, taxonomy ID: 2065218
Sequencing/Assembly provider ID: University of Colorado Boulder
Assembly date: 02 Jun 2025
Assembly type: haploid (haplotype 2)
Assembly level: Chromosome
Biosample: SAMN44478667
Assembly accession ID: GCA_050655635.1
Assembly FTP location: GCA/050/655/635/GCA_050655635.1_ASM5065563v1
Total assembly nucleotides: 37,500,256
Assembly contig count: 43
N50 size: 2,158,273
Clawson, H., Lee, B.T., Raney, B.J. et al.
"GenArk: towards a million UCSC genome browsers.
Genome Biol 24, 217 (2023).
https://doi.org/10.1186/s13059-023-03057-x
This download is only for the purpose of using this assembly hub in
your institution which may have firewall access restrictions to this
data.
To download this assembly data, use this rsync command:
rsync -a -P \ rsync://hgdownload.soe.ucsc.edu/hubs/GCA/050/655/635/GCA_050655635.1/ \ ./GCA_050655635.1/which creates the local directory: ./GCA_050655635.1/
wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \ --reject "index.html*" -P "GCA_050655635.1" \ https://hgdownload.soe.ucsc.edu/hubs/GCA/050/655/635/GCA_050655635.1/which creates a local directory: ./GCA_050655635.1/
There is an included hub.txt file in that download
data directory to use for your local track hub instance.
Using the genome browser menus: My Data -> Track Hubs
select the My Hubs tab to enter a URL
to this hub.txt file to attach this assembly hub to a genome browser.
The html/GCA_050655635.1_ASM5065563v1.description.html page is information for your users to
describe this assembly.
This web page with these instructions
is an instance of the html/GCA_050655635.1_ASM5065563v1.description.html file.
See also: track hub help documentation.
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 GCA_050655635.1.2bit file from:
https://hgdownload.soe.ucsc.edu/hubs/GCA/050/655/635/GCA_050655635.1/Which can be obtained with rsync via:
rsync -a -P rsync://hgdownload.soe.ucsc.edu/hubs/GCA/050/655/635/GCA_050655635.1/GCA_050655635.1.2bit ./With that GCA_050655635.1.2bit 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: GCA_050655635.1.someDna.psl
gfClient -t=dna -q=dna -genome=GCA_050655635.1 -genomeDataDir=GCA/050/655/635/GCA_050655635.1 dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa GCA_050655635.1.someDna.pslFor a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: GCA_050655635.1.someProtein.psl
gfClient -t=dnax -q=prot -genome=GCA_050655635.1 -genomeDataDir=GCA/050/655/635/GCA_050655635.1 dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa GCA_050655635.1.someProtein.psl
Search the assembly: