Scoring in PIMA

Paul Berti berti at cyclops.bri.nrc.ca
Thu Aug 20 14:27:36 EST 1992


Some time ago someone asked a question about PIMA (pattern induced multiple
alignment).  I've lost the original message, but here's my response
anyways.



>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

                                                                  -2
                _______________ 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. 


Paul
berti at bri.nrc.ca 




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