Protein Sequence Alignment Based on Fuzzy Arithmetic and Genetic Algorithm

In this paper a novel way to construct pairwise alignment of protein sequence is proposed. Currently in protein sequence alignment the vital problem is having too many uncertain factors and causes significant data loss while using crisp data. For this important premise, fuzzy concept is introduced and fuzziness is implemented in the matrix for 250 point accepted mutations (PAMs) in sequence aligning, and integrated with the genetic algorithm (GA). The purpose for this implementation is to reduce the effects of uncertain factor, avoid making use of crisp values or weights resulting in significant data loss, and increase solution accuracy and method suitability. Experimental results of fuzzy matrix for 250 PAM can find more continuous and identical protein sequence after sequence alignment by GA.

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