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I have the following quiz question, but the Pattern1 for both (ACC|ATA) and (CGA|ACT) are unique (just grep for ACC and CGA), which means it might be difficult to find the starting pattern for the DNA genome string in the following case. Do I need something like GapReduce algorithm ?

Quiz : There is a single (linear) string with the following (3,1)-mer composition. Find it.

(ACC|ATA) (ACT|ATT) (ATA|TGA) (ATT|TGA) (CAC|GAT) (CCG|TAC) (CGA|ACT)

(CTG|AGC) (CTG|TTC) (GAA|CTT) (GAT|CTG) (GAT|CTG) (TAC|GAT) (TCT|AAG)

(TGA|GCT) (TGA|TCT) (TTC|GAA)

k-d mer

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    Jul 7, 2022 at 15:48

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As shown in the picture in the question, just align the (k, d)-mers vertically without the help of assembler software, then compare whether they conflict with each other vertically.

Maybe the software to do such comparison uses https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

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    Jul 9, 2022 at 13:09

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