Consensus and Profile

In “Counting Point Mutations”, we calculated the minimum number of symbol mismatches between two strings of equal length to model the problem of finding the minimum number of point mutations occurring on the evolutionary path between two homologous strands of DNA. If we instead have several homologous strands that we wish to analyze simultaneously, then the natural problem is to find an average-case strand to represent the most likely common ancestor of the given strands.

Finding a Motif in DNA

Finding the same interval of DNA in the genomes of two different organisms (often taken from different species) is highly suggestive that the interval has the same function in both organisms.
We define a motif as such a commonly shared interval of DNA. A common task in molecular biology is to search an organism’s genome for a known motif.