By Topic

Design and Implementation of a Highly Parameterised FPGA-Based Skeleton for Pairwise Biological Sequence Alignment

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

3 Author(s)
Benkrid, K. ; Edinburgh Univ., Edinburgh ; Ying Liu ; Benkrid, A.

This paper presents the design and implementation of a generic and highly parameterised FPGA-based skeleton for pairwise biological sequence alignment. The skeleton is parameterised in terms of the sequence symbol type i.e. DNA, RNA, or protein sequences, the sequence lengths, the match score i.e. the score attributed to a symbol match or the penalty attributed to a mismatch or gap, and the matching task. Instances of the skeleton implement the Smith-Waterman and the Needleman-Wunsch algorithms. The skeleton has been captured in the Handel-C language which makes it FPGA-platform-independent. It implements the sequence alignment algorithm in hand using a pipeline of basic processing elements, which are tailored to the supplied parameters. Actual hardware implementations of the Smith-Waterman algorithm for protein sequence alignment achieve speed-ups in excess of 100:1 compared to equivalent standard desktop software implementations.

Published in:

Field-Programmable Custom Computing Machines, 2007. FCCM 2007. 15th Annual IEEE Symposium on

Date of Conference:

23-25 April 2007