When I say captures the hairpin best I am referring to the possible hairpin which encompasses the most residues because the end goal is to develop a general representation of any given sequence's secondary structure in terms of where hairpins pop up in the sequence. This will then be used to generate a kind of fingerprint that characterises a class of secondary structures. I have to disregard overlaps for the sake of simplicity, I am far too much of an amateur at programming to account for all the complexity in my data.

I didn't quite understand the historic threads regarding ranges too well. I'm still trying to get to grips with some of these computer science concepts. Although I think the 'state machine' might be useful, I think that it would then just be a matter of looping through the newly created hash of arrays and calculating the ranges and feeding the highest range into a final hash.

The thing is, is that I fear that all these loops are going to make it take a lifetime in the final analysis because I have about 140K sequences to go through with ~5+ hairpins, but for now, of course, I will test on small files.

I will try to see if I can loop through the hash to calculate and pick out max ranges.

Good luck me lol :/

Thanks for your help

In reply to Re^2: Making use of a hash of an array... by Peter Keystrokes
in thread Making use of a hash of an array... by Peter Keystrokes

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