Different approaches can be used to generate signatures. These include:
- hidden Markov models (HMMs)
Each approach starts with a protein multiple sequence alignment, and can focus on a single conserved sequence region (known as a motif), multiple conserved motifs, or the full alignment of the entire protein or a particular domain (see Figure 12).
Figure 12 Representation of different strategies for building signatures. A) single motif methods, B) multiple motif methods; and C) full alignment methods. Protein multiple sequence alignments are represented by black lines and the conserved regions used to build the signatures are indicated by coloured boxes.