الفهرس 
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Abstract
The emergence and development of the field of bioinformatics coincided with the production and accumulation of data in molecular biology. This class of programs is probably the most widely used and diverse class of programs in bioinformatics . These programs typically occupy the first chapters of relevant bioinformatics textbooks and the first few hours of most introductory lectures. Even simplest data manipulation tasks may become complicated as data quantity grows. To do that, we require specialized algorithms. A step-by-step computer process for addressing a problem is referred to as an ”algorithm.”
For instance, it looks simply to store a lot of DNA sequence data in computer databases. When the database is large, it becomes less trivial or even difficult to ask whether a new sequence segment (known as a query) has already been put in the database. Even more challenging is when we look not just at the sequence segments that perfectly match the query but also at those sequences that resemble the query. This is the purpose of sequence analysis.
Multiple Sequence Alignment has become an important topic in bioinfomatics. Sequence similarity is measured by taking into account all feasible sequence alignments and selecting the one where the ”distance” between the sequences is the smallest. Multiple Sequence Alignment is a significant modelling tool that has required solving a very difficult combination of computational