Re^2: Divide array of integers into most similar value halves

I'm not sure how to explain this... I have DNA sequence alignments, something like sequences of letter piled up so the similar bases (letters) are in top of each other. Then, each sequence has assigned a quality scores.
Something like:

A(45) C(44) T(44) A(45)
A(31) T(31) T(35) A(37)
A(50) C(52) A(52) A(52)

I'm looking for variation in those sequences, but in order to find variation that is reliable I've calculated that I need to find groups of sequences with the same base that add up to at least quality 50.
So in the previous example the second column C(44+52=96)/T(31) does not have enough quality to be considered (only one of the bases reaches the required quality), but the third column T(44+35=79)/A(52) does.
With your script I was trying to estimate how many of those positions in the alignment can I even consider analyzing, ie. how many of those positions (array of quality scores) can be separated in two subarrays that pass the threshold.
Sorry if it's not clear.

Pepe

Comment on Re^2: Divide array of integers into most similar value halves

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Re^3: Divide array of integers into most similar value halves by FunkyMonk (Bishop) on Sep 02, 2008 at 22:29 UTC
That was clear enough, thanks. I normally switch off as soon as I've read "CATG" 20 times over :-)	[reply]
Re^4: Divide array of integers into most similar value halves by Pepe (Sexton) on Sep 02, 2008 at 22:46 UTC
I know... That's why I didn't want to go into detail... Anyway, you guys have been of great help. I really appreciate it. Thanks. Pepe	[reply]