RNA secondary structure as a reusable interface to biological information resources

Area of Science:

• Bioinformatics
• Computational Biology
• Web Technologies

Background:

• Biological information dissemination increasingly relies on the Internet and World Wide Web (WWW).
• Current biologist-web interactions are often limited to basic interfaces like hypertext links and forms.
• Sophisticated WWW-based user interfaces are enabled by platform-independent runtime environments.

Purpose of the Study:

• To develop reusable, sophisticated WWW-based user interfaces for biological information.
• To leverage intuitive graphical representations of biological knowledge, termed "domain graphics," as interface elements.
• To demonstrate the versatility of domain graphics by creating an RNA secondary structure interface.

Main Methods:

• Developed a reusable interface based on the standard two-dimensional (2D) layout of RNA secondary structure.
• Designed the interface to represent pre-computed RNA layouts and accept user interaction parameters.
• Enabled the interface to provide information about selected bases, helices, or subsequences to associated applications.

Main Results:

• Created a versatile interface adaptable to various RNA data.
• Demonstrated the interface's utility as a specialized front-end for BLAST, Medline, and RNA MFOLD.
• Showcased the potential of domain graphics for intuitive biological data exploration.

Conclusions:

• Domain graphics offer a powerful approach for creating multipurpose, intuitive WWW-based biological user interfaces.
• Reusable graphical components can be effectively integrated with existing biological databases and computational engines.
• This approach enhances biologist interaction with complex biological information and computational tools.