Can I use nwalign to align one sequence to the reverse-complement of a second sequence?

I want to see if single stranded DNA will fold back on itself. I know I can just reverse-complement the sequence first, then call nwalign, but I want the alignment to show complementary bases aligning, not matching bases. I tried creating a modified version of the nuc44 scoring matrix, giving AT, TA, GC, CG all weight 5 and other weight -4, but that didn't seem to work. I assume the order in nuc44 is ATGCSWRYKMBVHDN.

Answer 1

[Luuk van Oosten]

Dear Dan Allison,

Wouldn't it be easier if you use the oligoprop function and see if your oligo's form hairpins or dimerize?

Let us take the [personalized] example from MATLAB's oligoprop page:

Dan = oligoprop('ACGTAGAGGACGTN')

and inspect Dan:

Dan = 

struct with fields:

                GC: 53.5714
           GCdelta: 3.5714
          Hairpins: 'ACGTagaggACGTn'
            Dimers: [3×14 char]
         etc etc etc etc

So in this case, yes, there are hairpins.

[Dan Allison]

Thanks for the response. I was not aware of the oligoprop function. I see that it does identify some hairpins, but not all the same ones that the mFold software does. I'll play around with some of the input settings since I'm just using the defaults for now.