Protein microarrays allow biologist to measure the characteristics of amino acid sequence on a small chip. It generates voluminous of data and new intelligent methods are needed to analyze them. Sequence alignment is challenging task for protein structure prediction. Also for better structural alignments, various algorithms have been proposed. In this paper familiar pair wise alignments are discussed and their significant merits and demerits Finally, this study concludes with an analysis of challenges to overcome for similarity mismatch of given candidate query is evaluated in every structural organization with conventional techniques that still remain to be resolved with Dynamic approach.