This is probably a naive question.
I have accesssed the Clustal Omega online multiple sequence alignment tool at http://www.ebi.ac.uk/Tools/msa/clustalo/ for the first time, but I think I need to provide more input to get it to do what I want, by specifying more constraints.
Edited to clarify constraints:
The original sequence P sequence has four symbols, say A,B,C,D.
The algorithm has access to 4 derived sequences.
P1: all occurrences of A,B deleted, no other change
P2: all occurrences of A,D deleted, no other change
P3: all occurrences of C,D deleted, no other change
P4: all occurrences of B,C deleted, no other change
Goal: given P1,P2,P3,P4, recover P
Note that I have removed the under bars by which I had tried to indicate deleted symbols but since the deletion processes for the Pi are deterministic they can be supplied to Clustal or whichever tool is appropriate.
End of edit
Toy madeup example illustrating my input, the output, and the problem.
The actual sequence from which these sequences came after deletions, followed by the resulting sequences is as below:
so I input
>p1 AACA >p2 BAAC >p3 ACBA
and got the output
p1 _AACA_ p2 BAAC__ p3 __ACBA **
Which is entirely reasonable, but I have constraints.
I want to align with the constraints that
- for certain symbols matches between certain sequence pairs should be maximized, and
- for certain symbols mismatches between certain sequence pairs are allowed
In fact given p1,p2,p3,p4, which all arose from p after deletions, there are the pairwise constraints
- A should be a match between p3 and p4 (it never appears in p1 or p2)
- B should be a match between p2 and p3 (it never appears in p1 or p4)
- C should be a match between p1 and p2 (it never appears in p3 or p4)
- D should be a match between p1 and p4 (it never appears in p2 or p3)
This means that p1 has only C,D; p2 has only B,C; p3 has only A,B; and p4 has only A,D characters after deletion.
I want to obtain the most likely alignment or a few most likely alignments of p1,p2,p3,p4 under these constraints.
I have looked to see if I could figure out how to input the constraints but no luck.
Should I have used another tool? In general I will have much longer sequences, typically 4 of them, with pairwise agree/disagree constraints, as stated above.