Gene analogue finder: a GRID solution for finding functionally analogous gene products

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Over 2.1 million gene products from 100,000+ species are described using the Gene Ontology (GO).
• GO enables functional comparisons of gene products beyond sequence similarity.
• Large-scale functional comparisons are computationally intensive.

Purpose of the Study:

• To develop a method for comparing gene products based on functional descriptions in GO.
• To leverage computational GRID resources for intensive data analysis.
• To identify functional analogues of gene products across species.

Main Methods:

• Developed GENe AnaloGue FINdEr (ENGINE) tool.
• Utilized computational GRID for parallelized processing and data distribution.
• Split analysis into sub-processes for efficient computation.

Main Results:

• ENGINE completed a large-scale functional comparison in 3 days, a task that would take over 5 CPU years on a single machine.
• Identified potential functional analogues for over 79,000 gene products.
• 46% of analyzed gene products yielded functional analogues, including novel associations.

Conclusions:

• ENGINE successfully demonstrates the potential of GO for identifying functional gene relationships.
• The quality of GO associations for non-model organisms is a current limitation.
• Future applications to the entire GO database promise to reveal extensive functional insights.