Share this genome browser with the link: https://http_host/h/GCA_016413895.1
Common name: cultivated vanilla
Taxonomic name: Vanilla planifolia, taxonomy ID: 51239
Sequencing/Assembly provider ID: Elo Life Systems
Assembly date: 28 Dec 2020
Assembly type: haploid (principal pseudohaplotype of diploid)
Assembly level: Chromosome
Biosample: SAMN14973820
Assembly accession ID: GCA_016413895.1
Assembly FTP location: GCA/016/413/895/GCA_016413895.1_Elo_Vpla-A_principal_1.0
Total assembly nucleotides: 736,752,966
Assembly contig count: 667
N50 size: 42,013,519

Data file downloads

GCA_016413895.1.fa.gz fasta sequence with NCBI GenBank sequence names
GCA_016413895.1.2bit UCSC 2bit sequence file with NCBI GenBank sequence names
GCA_016413895.1.chromAlias.txt chromAlias file to relate chromosome names
GCA_016413895.1_Elo_Vpla-A_principal_1.0.augustus.gtf.gz gene GTF file
GCA_016413895.1_Elo_Vpla-A_principal_1.0.xenoRefGene.gtf.gz gene GTF file
explore the hub directory at: hgdownload.soe.ucsc.edu/hubs/GCA/016/413/895/GCA_016413895.1/

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/016/413/895/GCA_016413895.1/ \
      ./GCA_016413895.1/

which creates the local directory: ./GCA_016413895.1/
or this wget command:

  wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \
    --reject "index.html*" -P "GCA_016413895.1" \
       https://hgdownload.soe.ucsc.edu/hubs/GCA/016/413/895/GCA_016413895.1/

which creates a local directory: ./GCA_016413895.1/

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_016413895.1_Elo_Vpla-A_principal_1.0.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_016413895.1_Elo_Vpla-A_principal_1.0.description.html file.

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_016413895.1.2bit file from:

  https://hgdownload.soe.ucsc.edu/hubs/GCA/016/413/895/GCA_016413895.1/

Which can be obtained with rsync via:

  rsync -a -P 
    rsync://hgdownload.soe.ucsc.edu/hubs/GCA/016/413/895/GCA_016413895.1/GCA_016413895.1.2bit ./

With that GCA_016413895.1.2bit 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_016413895.1.someDna.psl

gfClient -t=dna -q=dna -genome=GCA_016413895.1 -genomeDataDir=GCA/016/413/895/GCA_016413895.1 
    dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa GCA_016413895.1.someDna.psl

For a protein fasta query with your protein sequence in the file: someProtein.faa with result in the file: GCA_016413895.1.someProtein.psl

gfClient -t=dnax -q=prot  -genome=GCA_016413895.1 -genomeDataDir=GCA/016/413/895/GCA_016413895.1 
    dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa GCA_016413895.1.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.
By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.