Pairwise Sequence alignment and Multiple sequence alignment are the major challenges for the Bioinformatics application. In recent years there is good development and progress in this field by introducing good Tools or software’s, through which the High-Performance computing in alignment is achieved. This kind of alignment need a best Database for searching the protein’s and nucleotides. This paper talks about recent tools which evolved for Database searching and parallel computing of huge biological data. This is useful for the researchers or practitioners who are working for bioinformatics applications.