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Measurement aspects of genome pattern investigations - hardware implementation

Pułka A., Milik A.

Metrology and Measurement Systems

2012

Vol. 19, nr 1

49-62

The work presented in the paper concerns a very important problem of searching for string alignments. The authors show that the problem of a genome pattern alignment could be interpreted and defined as a measuring task, where the distance between two (or more) patterns is investigated. The problem originates from modern computation biology. Hardware-based implementations have been driving out software solutions in the field recently. The complex programmable devices have become very commonly applied. The paper introduces a new, optimized approach based on the Smith-Waterman dynamic programming algorithm. The original algorithm is modified in order to simplify data-path processing and take advantage of the properties offered by FPGA devices. The results obtained with the proposed methodology allow to reduce the size of the functional block and radically speed up the processing time. This approach is very competitive compared with other related works.

An Efficient Hardware Implementation of Smith-Waterman Algorithm Based on the Incremental Approach

Pułka A., Milik A.

International Journal of Electronics and Telecommunications

2011

Vol. 57, No. 4

489-496

The paper presents optimized hardware structure applied to genome alignment search. The proposed methodology is based on dynamic programming. The authors show how starting from the original Smith-Waterman approach, the algorithm can be optimized and the evaluation process simplified and speeded-up. The main idea is based on the observations of growth trends in the adjacent cells of the systolic array, which leads to the incremental approach. Moreover various coding styles are discussed and the best technique allowing further reduction of resources is selected. The entire processing unit utilizes fully pipelined structure that is well balanced trade-off between performance and resource requirements. The proposed technique is implemented in modern FPGA structures and obtained results proved efficiency of the methodology comparing to other approaches in the field.