CADO website Comparative Analysis of Protein Domain Organization

Draw domain graph

Compare domain graphs

Phylogenetic profiling

Withdraw proteins

Short introduction: CADO is a web server that allows users to visualize the protein domain organization in a given organism and compare domain organizations among different organisms. In the language of CADO, the organization of protein domains in a given organism is shown as a domain graph (demon) in which protein domains are represented as vertices and domain combinations, i.e. instances of two domains found in one protein, are represented as edges. CADO provides a simple way to study the function of domains based on their relations shown in the topology of domain graph, and a new way to analyze and compare whole proteomes in terms of domain organization (demon). Database: New! CADO has a built-in database of protein domain predictions of 311 (including 24 archaeal, 259 bacterial and 28 eukaryotic) genomes. [Genome list] [Domain list] Citation: Genome Research, 14:343-353, 2004 [Supplementary material to the paper]

Tools Create a domain graph from 'baiting domain(s)' Compare domain graphs of various organisms Generate phylogenetic profiles of domains and their combinations Search domains with similar or complementary phylogenetic profile Compare number of domain connections of various organisms Extract proteins in a genome that contain given domain(s)

Precalculated results The common/specific domain combinations List of hub-domains (sorted by connection degree) and modular-domains (sorted by clustering coefficient) Domain bridges (domain combinations that links two subclusters of domain) (big file!)

Godzik Laboratory | Burnham Institute | Questions/Comments

First set up: April, 4, 2003 | Latest update: Oct, 16, 2006