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An extensible automated protein annotation tool: standardizing input and output using validated XML.

S Vishnu V Deevi¹, Andrew C R Martin

¹School of Animal and Microbial Sciences, The University of Reading, P.O. Box 228, Whiteknights, Reading RG6 6AJ, UK.

Bioinformatics (Oxford, England)

|December 13, 2005

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A new tool dispatches biological sequences to various prediction and annotation services using a standardized XML format. This system streamlines the analysis of sequence data, making it more accessible for researchers.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Researchers frequently require diverse local or remote prediction and annotation tools for sequence analysis.
Existing tools often lack a unified data format, hindering interoperability.

Purpose of the Study:

To develop a tool for dispatching sequences to multiple services.
To establish a consistent XML format for sequence data and annotations.

Main Methods:

Designed XML Document Type Definitions (DTDs) to standardize input and output for annotation servers.
Developed plug-in wrappers for various services, integrated via a master script.
Formatted output (APATML) for HTML display and further post-analysis.

Main Results:

Related Experiment Videos

Annotations were categorized into six data forms: numeric/textual for residues, domains, or whole sequences.
A flexible XML structure was created to accommodate diverse annotation types.
The system successfully integrated multiple annotation services.

Conclusions:

The developed tool and XML format enable efficient and standardized analysis of biological sequences.
This approach enhances the utility of various prediction and annotation services by improving data integration.