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Maximum subarray problems arise in many fields, such as genomic sequence analysis and computer vision.. Genomic sequence analysis employs maximum subarray algorithms to identify important biological segments of protein sequences that have unusual properties, by assigning scores to points within the sequence that are positive when a motif to be recognized is present, and negative when it is not ...
A longest common subsequence (LCS) is the longest subsequence common to all sequences in a set of sequences (often just two sequences). It differs from the longest common substring : unlike substrings, subsequences are not required to occupy consecutive positions within the original sequences.
This subsequence has length six; the input sequence has no seven-member increasing subsequences. The longest increasing subsequence in this example is not the only solution: for instance, 0, 4, 6, 9, 11, 15 0, 2, 6, 9, 13, 15 0, 4, 6, 9, 13, 15. are other increasing subsequences of equal length in the same input sequence.
The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure .
One can find the lengths and starting positions of the longest common substrings of and in (+) time with the help of a generalized suffix tree.A faster algorithm can be achieved in the word RAM model of computation if the size of the input alphabet is in ( (+)).
The subset sum problem (SSP) is a decision problem in computer science.In its most general formulation, there is a multiset of integers and a target-sum , and the question is to decide whether any subset of the integers sum to precisely . [1]
This is a problem closely related to the longest common subsequence problem. Given two sequences X = < x 1,...,x m > and Y = < y 1,...,y n >, a sequence U = < u 1,...,u k > is a common supersequence of X and Y if items can be removed from U to produce X and Y. A shortest common supersequence (SCS) is a common supersequence of minimal length.
There is an optimization version of the partition problem, which is to partition the multiset S into two subsets S 1, S 2 such that the difference between the sum of elements in S 1 and the sum of elements in S 2 is minimized. The optimization version is NP-hard, but can be solved efficiently in practice. [4]