- Profile: frequency of each amino acid at each position is estimated

- Motif: a short signature pattern identified in the conserved region of the multiple alignment

- HMM: Hidden Markov Model, a generalized profile in rigorous
mathematical terms

1. Profile : a position-specific scoring matrix composed of 21 columns and N rows (N=length of sequences in multiple alignment)

Values of profile:

M(p,a)= Summa_{b=1}^{20 }W(p,b) x Y(a,b)

Y(a,b): Dayhoff matrix for *a* and *b* amino
acids

W(p,b): weight for amino acid b at position p.

- Profile can be used for searches against a database
(eg. SEARCHWISE)

2. Motif:

- several proteins are grouped together by similarity
searches

- they share a conserved motif

- motif is stringent enough to retrieve the family members
from the complete protein database

- PROSITE: a collection of motifs (1135 different motifs)

3. Hidden Markov Model:

- a composition of finite number of states,

- each corresponding to a column in a multiple alignment

- each state emits symbols, according to symbol-emission
probabilities

Starting from an initial state, a sequence of symbols
is generated by moving from state to state until an end stated is reached.