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CRT home > RbDe Web Service Tutorial: Secondary Structure Editor

Once you have imported a sequence and associated it with a layout in RbDe you can create a residue-based diagram for the sequence in advanced mode using the "Secondary Structure Editor".

[Note: When you select a layout other than "old-rbde" you can't access the Topology Editor that was available in previous versions of RbDe, since the topology is now dictated by the selected layout. To modify your diagram using the Topology Editor select "old-rbde" as your layout option.]

The secondary structure editor allows you to modify the positioning of the secondary structure elements indicated by the layout that you select.

A change to the content the editor triggers an update of the diagram that appears at the bottom of the page.

If the secondary structure elements for your sequence do not agree with those indicated in your selected layout, or cannot be predicted, a default set of secondary structure elements matching those indicated by the layout will be created for this sequence. You may customize these element positions as appropriate.

If you select either of the "GPCR" or "transporter" layouts, you have the option of selecting the "Fast diagram mode" which assumes that your sequence has helical transmembrane domains. The secondary structure editor can be accessed at any time by clicking the "Secondary Structure" button in the menubar.

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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Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
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