Today computational biology has merged with few other sciences for solving biological problems where there is a tremendous increment in innovations of new techniques and approaches that have been done day to day. In this field, area of research involves disease identification, sequence analysis, structural analysis, protein-protein interaction etc... in which pattern matching plays a major role. There are various tools that have been developed in pattern matching in the area of bioinformatics

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... r various analysis processes. At present bioinformatics tools are increasingly important to allow real-time decision making for solving biological problems for which performance plays the key role for evaluating the developed tools. Performance of a tool can be evaluated by means both qualitative and quantitative which has been involved in this paper. Quantitative based evaluation represents the quality of the tools for which metric based evaluation like specificity, sensitivity, pattern match etc... are been carried out. Qualitative based evaluation represents features, functionality evaluation together with the performance quantitative assessment. The merit that we are discovering by evaluating the existing products, leads us in the development of new products by avoiding the pitfalls of the existing products. In this work, some of the pattern tools are been considered for evaluating the performance which involves standards evaluation procedure. The results observed during this evaluations made on the specified tools have made an indication for having a standard development cum evaluation of pattern based bioinformatics tools. These evaluations could provide a way for developing and maintaining better systems with enhanced qualities.