strand complex prediction

Question

[pradeep.pant25]

Hi all,

I am having a single strand RNA lets say "AAUUAUAUAGCGCGGCC" and a chunk of RNA lets say "AUGC". The AUGC chunk is not a standard RNA but it is modified with no phosphates.

I want to see how their complex will look like, i.e. they will form double helix type complex or not by utilizing Watson-crick bonding (or some other bonding). Please do suggest in silico resources for such kind of study.

Any help would be highly appreciated!!

Answer 1

[Devon Ryan]

You can just use smith-waterman or needleman-wunsch. I would presume that the latter would be more useful with such short sequences. There's probably a biopython/bioperl function to do that, in fact.

BTW, RNA can do non-watson-crick pairing (namely A-A and G-U).

[pradeep.pant25]

Thanks but could you please explain in a little more detail as I am still not getting it.

[Devon Ryan]

What don't you get?

[pradeep.pant25]

I need to see the interactions between these two strands I mentioned in my question, I am not getting how Needleman-Wunsh Algo will help in that. Please may you explain.

[Devon Ryan]

Needleman-Wunsch is an alignment algorithm and you're looking for an alignment.