Trace back optimization for DNA sequence alignment using Viterbi algorithm

• Published in: International Journal of Simulation: Systems, Science and Technology
• Main Author: Saliman N.F.A.; Sabri N.D.A.; Al Junid S.A.M.; Halim A.K.; Abd Majid Z.; Md Tahir N.
• Format: Article
• Language: English
• Published: UK Simulation Society 2013
• Online Access: https://www.scopus.com/inward/record.uri?eid=2-s2.0-84963781053&doi=10.5013%2fIJSSST.a.14.06.06&partnerID=40&md5=b58cf398c889d6de33adc4c421cd318f

This paper presents two trace back design for DNA sequences alignment using Viterbi algorithm for Pair Hidden Markov Models (PairHMMs) and design optimization for reducing the utilizing design resources. The replacement of the dynamic matrix trace back determination with the Viterbi algorithm for PairHMMs and optimization has reduced the size of the design with the correct result when determine the optimal path for the sequences alignment at the optimal resource utilization. Altera Quartus II version 10.0 was used for compiling the design and targeting to EP4CE115F29C7 devices from Cyclone V E family. The trace back design simulation and verification were conducted using ModelSim Altera with the 30.15% and 323.53% utilizing design resource has been recorded with the implementation of Viterbi for PairHMMs with optimization produced the optimal result. © 2013, UK Simulation Society. All rights reserved.