Conserved Domains and Protein Classification
 
 
 
 
How to view the phylogenetic sequence tree for a conserved domain model
 
 

Interactive views of phylogenetic sequence trees for conserved domain models are available in NCBI-curated domains. If your domain of interest has an NCBI-curated model, you can retrieve it in the following way:

  • Search the Conserved Domain Database for your term(s) of interest, e.g., voltage gated chloride channel.

  • Limit your search results to NCBI-curated domains, which include interactive phylogenetic sequence trees, by adding the following criterion to your query at the top of the search results page:    AND cdd[Database],   and press the "Go" button.

  • Click on the accession number of any domain of interest on the search results page to open its CD summary page (example shown below).
  • A low resolution view of the phylogenetic sequence tree is embedded in the Sequence Cluster section of the CD summary page. Press the Zoom in button to view a higher resolution tree within the current browser window, or the Detailed View button to open a new browser window, which contains the higher resolution as well as options to highlight subsets of proteins by domain family tree node.

  • Alternatively, press either of the the Interactive Display buttons to open an interactive view of the phylogenetic sequence tree in the CDTree program. (The program must first be installed on your computer in order for those buttons to work. CDTree is a free helper application available for Windows and Macintosh platforms. Installation takes only a couple of minutes and help documentation, which describes the program's features and functions, is included in the program.)

  • It is also possible to embed a protein query sequence in a conserved domain model's phylogenetic sequence tree.

Illustration showing how to view the phylogenetic sequence tree of a conserved domain model, using the voltage gated chloride channel domain (cd00400) as an example.

 
 
 
 Revised 18 November 2014