Question: Implement the Planted motif(L,D) search problem in Java, for L = 9, D = 2, for 20 strings of length 600. The strings are derived
Implement the Planted motif(L,D) search problem in Java, for L = 9, D = 2, for 20 strings of length 600. The strings are derived from the dictionary {A, G, C, T}.
The steps of the algorithm are as folllows:
For each string i, find all substrings of length L and store in an array Si
For each array Si , Generate neighborhood (efficiently) of each substring in the array. Lets call it Ti.
Find all substrings x that occur in each of the Ti s.
(Generating neighborhood means that door D = 2 I can have 1-2 mismatches in the DNA sequence, so neighborhood is generated for every substring by first switching 1 character with alternatives and then 2 characters with their alternatives and all such patterns)
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