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Updated: Jun 22, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Mercury BLASTP: Accelerating Protein Sequence Alignment.

Arpith Jacob¹, Joseph Lancaster, Jeremy Buhler

¹Dept. of Computer Science and Engineering, Washington University in St. Louis.

ACM Transactions on Reconfigurable Technology and Systems

|June 4, 2009

Summary

This summary is machine-generated.

We developed Mercury BLASTP, a high-performance FPGA-accelerated version of BLASTP, to speed up protein sequence comparison. This new design runs 11-15 times faster than traditional software BLASTP.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Computational Biology
Bioinformatics
Molecular Biology

Background:

Large-scale protein sequence comparison is crucial but computationally demanding.
The exponential growth of protein databases strains existing tools like BLASTP.
High-performance computing solutions are needed to manage large biological datasets.

Purpose of the Study:

To design and implement a high-performance, FPGA-accelerated version of BLASTP.
To address the computational bottlenecks in protein sequence comparison.
To accelerate the analysis of rapidly growing protein sequence databases.

Main Methods:

Developed Mercury BLASTP, integrating FPGA-accelerated components with existing BLASTP software.
Utilized Xilinx Virtex-II 6000 FPGAs on a commodity workstation for acceleration.
Architected specific application portions for efficient FPGA execution.

Main Results:

Mercury BLASTP achieved 11-15 times speedup compared to software BLASTP on modern CPUs.
The FPGA-accelerated version maintained high accuracy, yielding close to 99% identical results.
Demonstrated the feasibility of using FPGAs to accelerate computationally intensive bioinformatics tasks.

Conclusions:

FPGA acceleration offers a significant performance improvement for protein sequence comparison.
Mercury BLASTP provides a viable solution for handling large-scale protein sequence data efficiently.
This approach enhances the speed of critical bioinformatics analyses without compromising accuracy.