ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Advanced software tools often face accessibility challenges due to hardware or expertise requirements.
• The internet provides a platform to overcome these distribution barriers for complex computational tools.

Purpose of the Study:

• To make the MEME (Multiple Em for Motif Elicitation) tool for discovering biological patterns accessible to a broader audience.
• To develop and deploy a web-based interface for a parallelized version of MEME.

Main Methods:

• Developed ParaMEME, a parallelized version of MEME using a single-program multiple-data approach.
• Deployed ParaMEME on an Intel Paragon XP/S parallel computer at the San Diego Supercomputer Center.
• Created a worldwide web interface for interactive sequence submission and results retrieval.

Main Results:

• ParaMEME demonstrates efficient scalability on parallel hardware, achieving over 72% efficiency on 64 nodes for large datasets.
• The web interface allows biologists to submit sequences and receive motif analysis results via email.
• The tool is available for free public use, enhancing accessibility for biological sequence analysis.

Conclusions:

• Web-based distribution significantly improves the accessibility of powerful bioinformatics software.
• ParaMEME offers a scalable and efficient solution for motif discovery in biological sequences.
• The project successfully bridges the gap between high-performance computing and the needs of the biological research community.