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Bioinformatics applications represent an increasingly important workload to improve the programs of sequence analysis. It can be used to assign function to genes and proteins by the study of the similarities between the compared sequences. This paper introduces a modified implementation of bioinformatics algorithm for sequence alignment .The implemented algorithm is called Fast Longest Common Subsequence (FLCS). It is filling the three main diagonals without filling the entire matrix by thedoi:10.5120/9419-3569 fatcat:fmoathbdkbcljmv74rdojer6r4