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I'm assuming we don't do pattern matching in DNA or RNA for the fun of it. So I'd like to know what are the applications of pattern matching or where does it fit in in larger applications?

I'm a computer scientist and when studying certain topics in CS we see a lot of references to applying algorithms to areas of biology or genetics one of which is applying text pattern matching algorithms to DNA to find sub sequences. Whenever I see those kinds of examples I think "Oh that's pretty cool" but then I don't see how it's applied in the real world for benefit and I can't find anything to suggest where these algorithms are applied in these fields.

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One useful application of pattern matching is for DNA sequence motifs. As an example of a direct application, there is a class of proteins called transcription factors (TFs), which bind to DNA and regulate the expression of genes. There are many TFs. Each TF likes to bind to its particular conserved sequence of DNA, with some wiggle room for some parts of the sequence.

Algorithms for finding and scoring these patterns (and mismatches in patterns) is important for identifying regions where regulation occurs, which proteins are involved, and for answering biological questions related to gene regulation and basic biological functionality — and malfunction, in case of disease.

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