Algorithm 1.

Require:  rawpssm, sequence

Ensure:  PSSM

1:  tag ← [A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y]

2:  Initialize index, PSSM

3:  n ← length(tag)

4:  l ← length(sequence)

5:  for i=0 → n-1 do

6:          Initialize num

7:          for key=0 → n-1 do

8:               index[tag[key]] = 0

9:          end for

10:          for j=0 → l-1 do

11:               index[sequence[j]] + = rawpssm[j, i]

12:          end for

13:          for k=0 → n-1 do

14:               num[k] ← index[tag[k]]

15:          end for

16:          PSSM[i] ← num

17:  end for

18:  PSSM ← PSSM / l