Share this genome browser with the link:  https://http_host/h/GCA_964188545.1  
Common name: southeastern Asian house mouse
Taxonomic name: Mus musculus castaneus, taxonomy ID: 10091
Sequencing/Assembly provider ID: EMBL-EBI, WELLCOME TRUST GENOME CAMPUS, CAMBRIDGE
Assembly date: 23 Jun 2024
Assembly type: haploid
Assembly level: Chromosome
Biosample: SAMEA115765482
Assembly accession ID: GCA_964188545.1
Assembly FTP location: GCA/964/188/545/GCA_964188545.1_CAST_EiJ_T2T_v1
Total assembly nucleotides: 2,950,550,120
Assembly contig count: 338
N50 size: 139,012,417

Data file downloads

Cite reference: To reference these resources in publications, please credit:

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

Copy this entire assembly hub for local use

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/964/188/545/GCA_964188545.1/ \
      ./GCA_964188545.1/
which creates the local directory: ./GCA_964188545.1/
or this wget command: 
  wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \
    --reject "index.html*" -P "GCA_964188545.1" \
       https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/545/GCA_964188545.1/
which creates a local directory: ./GCA_964188545.1/

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_964188545.1_CAST_EiJ_T2T_v1.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_964188545.1_CAST_EiJ_T2T_v1.description.html file.

See also: track hub help documentation.

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 GCA_964188545.1.2bit file from: 

  https://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/545/GCA_964188545.1/
Which can be obtained with rsync via: 
  rsync -a -P 
    rsync://hgdownload.soe.ucsc.edu/hubs/GCA/964/188/545/GCA_964188545.1/GCA_964188545.1.2bit ./
With that GCA_964188545.1.2bit 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_964188545.1.someDna.psl 
gfClient -t=dna -q=dna -genome=GCA_964188545.1 -genomeDataDir=GCA/964/188/545/GCA_964188545.1 
    dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa GCA_964188545.1.someDna.psl
For a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: GCA_964188545.1.someProtein.psl 
gfClient -t=dnax -q=prot  -genome=GCA_964188545.1 -genomeDataDir=GCA/964/188/545/GCA_964188545.1 
    dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa GCA_964188545.1.someProtein.psl

Search the assembly: