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ArchSchema description

 

ArchSchema plots the relationships between Pfam domain architectures. An architecture is defined as the sequence of Pfam domains common to a family of protein sequences. On the plot each architecture is represented by a node with the domains colour-coded, as shown in the examples below.

a.   b.   c.

The red underlines in (c) indicate the extent to which 3D structures of the domains and architectures are available in the PDB. Left-clicking on a node shows a panel containing information about the constituent domains, the protein sequences having the given architecture, and any sequences that have whole or partial structures in the PDB.

You can display protein sequence (or, alternatively, the protein structures) associated with each architecture, as in the examples below. Where there are too many sequence or structure nodes to show, a selection are shown and are colour pink (as in the third example).

UniProt sequences   PDB structures   Many satellite nodes

An example plot is shown below. Click on it to get a full-size version.

Acknowledgments: Archschema is built using the Prefuse open source, java-based, data visualization toolkit.

 

Written by: Asif Tamuri
Version: 1.0
Modified by: Roman Laskowski
Date: 17 July 2009

 

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