Generic FPGA core for Pairwise Sequence Alignment

Pairwise sequence alignment on a linear processor array

LICENSING OPPORTUNITY

Researchers at the University of Edinburgh have developed a highly parameterised FPGA core for pairwise biological sequence alignment that provides researchers with the ability to analyse large biological data in a reasonable timeframe.

This FPGA core for general pairwise sequence alignment provides speed-ups in excess of 100x than equivalent software implementations running on general purpose computers, and at a fraction of the power consumed. Hence, offering an efficacious and efficient computing platform for computationally intensive operations normally requiring a cluster of computers.

This is the most parameterizable FPGA core for pairwise sequence alignment ever reported in the literature, with performance figures matching the best reported results.

Speeds up of 150x have been demonstrated over a Dual-Core AMD OpteronTM processor 2218 using one Xilinx Virtex 4 LX160 -11 FPGA.

A hardware prototype of an FPGA-based web server for biological sequence alignment has been produced.

Key Benefits

Hardware implementations of a single FPGA core achieve, when compared to standard desktop software implementations
- 100x faster computation speed
- 180x Performance per Watt
- 5x Performance per $
Support for a variety of sequence types and codes, substitutions matrices, gap penalties and matching tasks
FPGA core can be used to efficiently implement a range of alignment algorithms e.g. Smith-Waterman and Needleman-Wunsch, with various flavours
FPGA platform independent. It can be optimized for specific FPGA series

Applications

Biological DNA/RNA/Protein sequence alignment in
- Computation Biology
- Crime Prosecution
Non-biological use of sequence alignment
- Natural language processing
- Data pattern matching in networking applications
- Data stream processing in high-end servers

IP Status

Khaled Benkrid, Ying Liu and AbdSamad Benkrid “A Highly Parameterized and Efficient FPGA-Based Skeleton for Pairwise Biological Sequence Alignment” IEEE Transactions on VLSI Systems, Volume 17, Issue 4, April 2009, pp. 561-570

The University of Edinburgh is seeking interest from commercial partners to in-license this IP core on a non-exclusive basis.

If you would like further information about this opportunity please fill out the form below. Your enquiry will be passed on to the relevant University who will respond to you directly.

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