(Photo courtesy of WikiMedia Commons: Alpsdrake)
Common name: lizards
Taxonomic name: Gekko japonicus, taxonomy ID: 146911
Sequencing/Assembly provider ID: Nantong University
Assembly date: 25 Nov 2015
Assembly type: haploid
Assembly level: Scaffold
Assembly accession ID: GCF_001447785.1
Assembly FTP location: GCF/001/447/785/GCF_001447785.1_Gekko_japonicus_V1.1
Total assembly nucleotides: 2,490,274,461
Assembly contig count: 191,500
N50 size: 707,733
This download is only for the purpose of using this assembly hub in
your institution which may have firewall access restrictions to this
To download this assembly data, use this rsync command:
rsync -a -P \ rsync://hgdownload.soe.ucsc.edu/hubs/GCF/001/447/785/GCF_001447785.1/ \ ./GCF_001447785.1/which creates the local directory: ./GCF_001447785.1/
wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \ --reject "index.html*" -P "GCF_001447785.1" \ https://hgdownload.soe.ucsc.edu/hubs/GCF/001/447/785/GCF_001447785.1/which creates a local directory: ./GCF_001447785.1/
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/GCF_001447785.1_Gekko_japonicus_V1.1.description.html page is information for your users to
describe this assembly.
This web page with these instructions is an instance of the html/GCF_001447785.1_Gekko_japonicus_V1.1.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 GCF_001447785.1.2bit file from:
https://hgdownload.soe.ucsc.edu/hubs/GCF/001/447/785/GCF_001447785.1/Which can be obtained with rsync via:
rsync -a -P rsync://hgdownload.soe.ucsc.edu/hubs/GCF/001/447/785/GCF_001447785.1/GCF_001447785.1.2bit ./With that GCF_001447785.1.2bit 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: GCF_001447785.1.someDna.psl
gfClient -t=dna -q=dna -genome=GCF_001447785.1 -genomeDataDir=GCF/001/447/785/GCF_001447785.1 dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa GCF_001447785.1.someDna.pslFor a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: GCF_001447785.1.someProtein.psl
gfClient -t=dnax -q=prot -genome=GCF_001447785.1 -genomeDataDir=GCF/001/447/785/GCF_001447785.1 dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa GCF_001447785.1.someProtein.psl
Search the assembly: