FPGA Implementation of the FM-Index String Matching algorithm

This book discusses the research processes of developing a hardware implementation of a string matching algorithm. The first phase of the research is qualifying the appropriate algorithm for the application of DNA sequence matching. The second phase is re-inventing the algorithm to make it suitable for a hardware implementation. The third phase is implementing the chosen algorithm using FPGAs. The last phase is measuring performance using real data sets for comparison to other known tools. Our implementation shows a real time speedup up of up to 70x against BOWTIE, a known tool used in sequence matching.

About the author

Dr Edward Bryann C Fernandez earned B.S. in Computer Engineering and M.S. Electrical Engineering from the University of the Philippines in 2002 and 2007 respectively. He earned his doctorate degree from the University of California in Riverside in 2012. He is currently working as Design Engineer for Freescale, a semiconductor company.

Product details

• Authors: Edward Bryann Fernandez
• Publisher: Scholar's Press
• Languages: English, German
• Product format: Paperback / Softback
• Released: 20.11.2013
• EAN: 9783639702781
• ISBN: 978-3-639-70278-1
• No. of pages: 140
• Dimensions: 150 mm x 220 mm x 8 mm
• Weight: 227 g
• Subject: Natural sciences, medicine, IT, technology > Biology > Genetics, genetic engineering