The analysis of multiple DNA or protein sequences (I)

The analysis of multiple DNA or protein sequences (I) Sequence similarity is an important issue in sequence alignments. In molecular biology, proteins and DNA can be similar with respect to their function, their structure, or their primary sequence of amino or nucleic acids. The general rule is that sequence determines shape, and shape determines function. So when we study sequence similarity, we eventually hope to discover or validate similarity in shape and function. This approach is often successful. However, there are many examples where two sequences have little or no similarity, but still the molecules fold into the same shape and share the same function. This lecture speaks of neither shape nor function. We are focusing on DNA sequences. Sequences are seen as strings of characters. In fact, the ideas and techniques we discuss in this lecture have important applications in text processing, too. Similarity has both a quantitative and a qualitative aspect: A similarity measure gives a quantitative answer, saying that two sequences show a certain degree of similarity. An alignment is a mutual arrangement of two sequences which is a sort of qualitative answer; it exhibits where the two sequences are similar, and where they differ. An optimal alignment, of course, is one that exhibits the most correspondences, and the least differences.