Recent Advances in the Walking Tree Method for Biological Sequence Alignment

2003 ◽  
pp. 349-359 ◽  
Author(s):  
Paul Cull ◽  
Tai Hsu
Keyword(s):  
Sequence Alignment ◽  
Biological Sequence ◽  
Recent Advances ◽  
Tree Method

An Efficient Scheduling Technique for Biological Sequence Alignment

2015 ◽  
Vol 754-755 ◽  
pp. 1087-1092
Author(s):  
Mohd Nazrin Md Isa ◽  
Sohiful Anuar Zainol Murad ◽  
Mohamad Imran Ahmad ◽  
Muhammad M. Ramli ◽  
Rizalafande Che Ismail
Keyword(s):  
Sequence Alignment ◽  
Substitution Matrix ◽  
Processing Element ◽  
Biological Sequence ◽  
Matrix Computation ◽  
Logic Block ◽  
Order Of Magnitude ◽  
Speed Up ◽  
A New Technique ◽  
Protein Sequencer

Computing alignment matrix score to search for regions of homology between biological sequences is time consuming task. This is due to the recursive nature of the dynamic programming-based algorithms such as the Smith-Waterman and the Needleman-Wunsch algorithmns. Typical FPGA-based protein sequencer comprises of two main logic blocks. One for computing alignment scores i.e. the processing element (PE), while another logic block for configuring the PE with coefficients. During alignment matrix computation, the logic block for configuring the PE are left unused until the time consuming alignment matrix computation finished. Therefore, a new technique, known as overlap computation and configuration (OCC) is proposed to minimize the time overhead for performing biological sequence alignment. The OCC technique simultaneously updating substitution matrix in a processing element (PE) systolic array, while computing alignment matrix scores. Results showed that, the sequencer achieves more than two order of magnitude speed-up higher compared to the state of the art, at negligible area overhead, if any.

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