# Online multiple sequence alignment with constraints

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.

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

Example

P1 CCDDCC

P2 BCCCBBC

P3 ABAAABB

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:

p ABACBAC

p1 A_AC_A_

p2 _BA__AC

p3 __ACBA_

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.

• This question is unclear. What do you mean by A,B, C and D? Are these residues, or points in a list. I think you should expand on your toy sequences.Assuming you can't post your actual sequences, perhaps use another real peptide and make up similar constraints to the ones in your own problem (although I still don't understand what your constraints are). Apr 17, 2016 at 2:59
• I also don't understand your constraints. Also, why do you need constraints? Usually when you do MSA, you don't pose any constraints since you presumably don't know how the query sequences can be aligned. Also, I bet that if you include sequence "p" in your MSA, the alignment will be different and will include your constraints. Apr 17, 2016 at 5:10
• @James, thanks for your comments, I will re-edit the question to clarify. Apr 17, 2016 at 22:04
• @GerganaVandova, thanks, will rephrase the question. Apr 17, 2016 at 22:05