Part of   Helix

SStructView: RNA Secondary Structure Java Applet

Site Directory

• SStructView 1.2
  • QuickStart gets you up and running with SStructView on your own web site.
  • Home Page includes a pointer to the Java class files.
  • Technical Documentation
  • BLAST Demos.
• SStructView 1.1
  • Home Page includes a pointer to the Java class files.
  • Version 1.1 Tutorial including JavaScript demo.
  • Technical Documentation
  • BLAST Demos.
• SStructView 1.0
  • Home Page includes a pointer to the Java source and class files.
  • Demos for molecular biology, basic CGI support, and a PS conversion script.
• Sample Data Files
  • E. Coli RNA 16S data file.
  • E. Coli RNA 23S data file.
  • E. Coli RNA 16S data file with customized objects (only for v1.1).
  • E. Coli RNA 16S data file with customized objects and colored bases (only for v1.2 or later).
• Other
  • SStructView Wish List and Feature Requests.

Publications

SStructView's features and implementation were first described in our manuscript RNA Secondary Structure as a Reusable Interface to Biological Information Resources (Gene 190 (1997) GC59-70). Also available on-line in Gene-COMBIS. This abstract from the paper describes and motivates SStructView:

The dissemination of biological information has become critically dependent on the Internet and World Wide Web (WWW), which enable distributed access to information in a platform independent manner. The mode of interaction between biologists and on-line information resources, however, has been mostly limited to simple interface technologies such has hypertext links, tables and forms. The introduction of platform-independent runtime environments facilitates the development of more sophisticated WWW-based user interfaces. Until recently, most such interfaces have been tightly coupled to the underlying computation engines, and not separated as reusable components. We believe that many subdisciplines of biology have intuitive and familiar graphical representations of knowledge that can serve as multipurpose user interface elements. We call such graphical idioms "domain graphics." In order to illustrate the power of such graphics, we have built a reusable interface based on the standard two dimensional (2D) layout of RNA secondary structure. The interface can be used to represent any pre-computed layout of RNA, and takes as a parameters the sets of actions to be performed as a user interacts with the interface. It can provide to any associated application program information about the base, helix, or subsequence selected by the user. We show the versatility of this interface by using it as a special purpose interface to BLAST, Medline and the RNA MFOLD search/compute engines.

Availability

R. M. Felciano, R. O. Chen, & R. B. Altman. RNA Secondary Structure as a Reusable Interface to Biological Information Resources. 1997. (Gene 190 (1997) GC59-70) SMI Tech Report SMI-96-0641

Credits

This is work by Ramon M. Felciano, Richard Chen and Russ Altman, Helix Group, SMI. The secondary structure graphics shown in these pages are based on those provided by Dr. Robin Gutell at 16S rRNA secondary structure site. Authors were supported under grants NSF-BIR9600637 and NIH-LM06244.