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Optimal alignment of two sequences 2

Write a program that calculates the similarity of two nucleotide sequences and their best global alignment for the following cases: a) in a model with an arbitrary gap penalty function (this function should be set in the code; should also work for non-linear functions!), and b) in a model without a gap penalty function, but using an algorithm of linear memory complexity. Data should be read from a file. Data includes: 2 sequences and similarity matrix between nucleotides. The output of the program should contain the optimal alignment and its similarity

Skills: Java

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