Rhododendron Research Network Logo ARS

Rhododendron Research Network


 

Search the Rhododendron Genome with BLAST

Two chromosome-level genome assemblies for Rhododendron (R. simsii and R. williamsianum) have been deposited at the National Center for Biotechnology Information (NCBI) for public use. You can search these genomes for DNA or protein sequences that are similar to a sequence or gene of interest using NCBI's online BLAST (Basic Local Alignment Search Tool).

How to use BLAST

You will need a DNA or protein sequence that you want to search for in these genomes. The BLAST results will include similar sequences found in the genome and the location of these sequences in the genome.

To use a DNA sequence to search, paste it into the "Enter Query Sequence" box, or "Choose File" on the "blastn" tab and select "Somewhat similar sequences (blastn)" as your best bet for results before hitting the "BLAST" button.

To use a protein sequence to search, paste it into the "Enter Query Sequence" box, or "Choose File" on the "tblastn" tab and hit the "BLAST" button.

BLAST results will be provided in "Descriptions", "Graphic Summary" and "Alignments" tabs. Descriptions will give you a summary of the top hits to your query, showing you which chromosomes (also known as LGs for linkage groups) have similar sequences to your query. The lower the E value, the better the hit. You can click on each hit to see how your query sequence matches the genome ("subject") sequence. This same information is provided in the Alignments tab, which shows which part of your query sequence matches which part of the genome sequence, as denoted by nucleotide or amino acid positions at the left and right ends of the aligned sequences. Graphic Summary shows you how long your query sequence is and which part matches the "subject" sequences found in the genome. You can click on the colored subject sequences in Graphic Summary to get to their alignments as well.

If you want to download a matching genomic sequence in its entirety, click on the Accession number under Descriptions. Then select "Send to:", "Complete Record", "File", "Format"="Fasta", then "Create File".

BLAST search the:

R. williamsianum genome

R. simsii genome.

Return to Research Network Home Page


American Rhododendron Society
P.O. Box 214, Great River, NY 11739
Website: www.rhododendron.org
Ph: 631-533-0375   Fax: 866-883-8019   E-Mail: member@arsoffice.org
1998-2020, ARS, All rights reserved.