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!!
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pradeep.pant25 •
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).
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Devon Ryan
Thanks but could you please explain in a little more detail as I am still not getting it.
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pradeep.pant25 •
What don't you get?
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Devon Ryan
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.
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pradeep.pant25 •
Needleman-Wunsch is an alignment algorithm and you're looking for an alignment.
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Devon Ryan
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