Some time ago someone asked a question about PIMA (pattern induced multiple
alignment). I've lost the original message, but here's my response
>Also... doesn't PIMA work with coding sequences when aligning proteins, or
>something like that? Anyone know?
No, not quite. PIMA's scoring scheme is shown below (from the manual):
Amino Acid Classes Match score
_______________ X __________________ 0
/ / \ \
_ f _ / ______r _______ \ 1
/ / \ / / / \ \ \
/ c \ e / m p \ _ j __ 2
/ / \ \ / \ / / \ / \ \ / \ \
/ a b d \ / l k o n i h \ 3
/ / \ / \ /|\ \ / / \ / \ / \ /\ / \ / \ \
C I V L M F W Y H N D E Q K R S T A G P 5
Note: During clustering, matches between unrelated amino
acids, i.e. connected only through the 'X' (wild-card)
class, score -2
This means that all amino acids score 5 when aligned against themselves.
Other a.a.'s are scored according to the above diagram: e.g. consider
Asn (N). It scores 5 aligned against itself, 3 against D, 2 against E,
1 against H, Q, K, R, S, & T and 0 against everything else.
I hope this helps.
b.t.w. - I've been using PIMA for a few weeks now (in fact it's running
in another window right now); it's the best multiple alignment program
I've seen, bar none.
berti at bri.nrc.ca