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

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Dan Allison
Dan Allison on 9 Mar 2017
Commented: Dan Allison on 13 Mar 2017
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.

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Answers (1)

Luuk van Oosten
Luuk van Oosten on 10 Mar 2017
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.

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Dan Allison
Dan Allison on 13 Mar 2017
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.

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