Remember the flow of genetic information in a cell is from DNA to RNA and finally to proteins. The DNA is transcribed into discrete, essentially gene-sized, pieces of RNA which are then translated into a sequence of amino acids. These will fold into a complex three-dimensional protein structure and may be further modified before they are fully matured into functioning proteins. However, despite the fact that proteins are not translated directly from DNA, most sequence analysis is performed on the DNA sequence and so we will adopt the conventions of DNA rather than RNA in the discussions in this chapter, referring to thymine rather than uracil.