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CRT home > RbDe Web Service Tutorial: Topology Editor

Once you have imported a sequence and selected the "old-rbde" layout you can modify your residue-based diagram using the "topology editor".
[Note: The production version of RbDe does not have the layout feature and employs the Topology Editor for editing residue based diagrams]

The Topology Editor allows you to define or refine the topology and secondary structure of the sequence you want to draw a diagram for. The editor is made of three parts, shown below. A change to the content of one of these editors triggers the update of the diagram that appears at the bottom of the page. (No diagram is displayed unless the secondary structure contains at least one element.) The topology editor can be accessed from the "Sequence Display" page by clicking on the "Advanced diagram mode", or from by clicking the "Secondary Structure" button in the menubar.

First, define the transmembrane (TM) segments, using the right panel "TM Segment Editor". This editor allows you to define the transmembrane segments for a given sequence. Depending on the way you imported the sequence in RbDe, the editor can show no TM segments or the TM segments that were described in the sequence annotation.

Then, define the secondary structure with the TM segments which should be shown. To do this, click the "Assume transmembrane segments are helices" link in the top panel, or use the "secondary structure editor" in the left panel. This editor allows you to add and remove elements of secondary structure on the diagram.

Alternatively, you may use one of the transmembrane prediction methods available to predict the transmembrane elements for your sequence.

The transmembrane layout engine requires you to adhere to a few simple rules to create a diagram:

You need at least one secondary structure element for every primary structure element. The links "Assume transmembrane segments are helices" and "Assume defined elements of secondary structure are transmembrane segments" can help to ensure that this constraint is met.

The limits of the secondary structure should be less than or equal to the residue position limits of the TM segment.

Secondary structure elements with limits within the limits of a TM segment are rendered vertically, otherwise the secondary structure is rendered horizontally.

Registered users can save their diagrams in the diagram library and also change specific diagram attributes of saved diagrams.

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

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