missing predecessor arrows?

[sjanssen2]

Hi Freiburg team,

I love your alignment resources for teaching! Thanks for this great service.

When I am using Gotoh and click one an arbitrary cell in one of the three DP matrices, I assume that the outgoing arrows indicate the predecessor cells. If that is the case, shouldn"t there be two arrows in every P-entry / Q-entry and three for every D-entry? On my browser (tested Firefox and Chrome) under Ubunutu 20.4, I can only spot n-1.

Unfortunately, I cannot attach a screenshot through this form. Let"s see if I can send it to you via mail.

Best, Stefan

[martin-raden]

Hi @sjanssen2

many thanks for your feedback.

All arrows in the matrices represent optimal tracebacks, ie. not computation ways but traces that produce the value within the clicked cell.

Thus, I hope the two trace arrows in your marked cell are the only options to produce the cell's value of 7:

• either D(-4) + gapopening(-2) + gaplengthcost(1*-1)
• or P(-6) + gapextension(-1)

the P recursion has only these two options anyway..

for D three traces are possible, but often only one is the optional one. thus you find between one and three trace arrows starting in D cells..

does this makes sense? :)

Best, Martin

[sjanssen2]

makes total sense - I simply made a wrong assumption. You might want to add a description of those arrows. It would be helpful to have another type of arrows for predecessor cells though :-)