institute for computational biomedicine : RbDe

CRT home > RbDe Web Service Tutorial: Visualizing a sequence

This page presents the sequence that is currently being used to construct a diagram. You will see it just after importing a sequence (so that you can check that the sequence you have entered is the one you actually intended to enter) or when you select the "view sequence" button from the menu bar on top of an RbDe page.

The page presents the short name of the sequence (OPSD_HUMAN is shown in the illustration), the length of the sequence (348 here) and the actual sequence of residues that is used to build the diagram.

In the production version of RbDe:
After viewing the sequence, the user is able to use the sequence to build a diagram with one of the following options:

The "Fast diagram mode" assumes that the transmembrane domains are helical. The diagram is then rendered and you have the ability to change parameters using the "Advanced diagram mode".

The "Advanced diagram mode" features a topology editor that allows modification of secondary structure for specific transmembrane segments in the imported sequence.

Further Information about the algorithms used to automate the diagram building processes in RbDe, please read a description of the algorithms.

In the beta version of RbDe:
The user is able to select a layout for the diagram before proceeding to draw it and/or modify the positioning of the secondary structure elements indicated by selected layout.

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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Events

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
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301