WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance...

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Gene function discovery relies on sequence homology searches against protein databases.
• Next-generation sequencing enables genome-wide gene expression studies (RNA-seq, metagenomics).
• Large-scale functional annotation is computationally intensive, often requiring days for results.

Purpose of the Study:

• To develop a user-friendly web interface for mpiBLAST, a parallelized BLAST program.
• To simplify the use of high-performance computing (HPC) clusters for large-scale sequence similarity searches.
• To accelerate the computationally intensive process of gene functional annotation for biologists.

Main Methods:

• Developed WImpiBLAST, an open-source web interface using Struts 1.3 and Java.
• Implemented features for script creation, job submission, and monitoring.
• Integrated with the Torque resource manager on a Linux-based HPC cluster.

Main Results:

• WImpiBLAST offers a simplified approach to utilizing mpiBLAST for parallel sequence similarity searches.
• The web interface addresses the lack of user-friendly tools for biologists needing HPC resources.
• Demonstrated significant acceleration of annotation analysis through use case examples.

Conclusions:

• WImpiBLAST enhances accessibility to powerful parallel computing for biological sequence analysis.
• The tool facilitates faster and more efficient functional annotation of genes.
• It empowers biologists to leverage HPC for large-scale genomic data analysis without extensive command-line expertise.