On 3/2/2012 2:11 PM, Hs Hs wrote:
Hi:
I have the following table and I am interested in calculating mismatch
ratio. I am not completely clear how to do this and any help is deeply
appreciated.
Length Matches
77 24A0T9T36
71 25^T9^T37
60 25^T9^T26
62 42A19
In length column I have length of the character string.
In the second column I have the matches my reference string.
In fist case, where 77 is length, in matches from left to right, first
24 matched my reference string following by a extra character A, a
null (does not account to proble) and extra T, 9 matches, extra T and
36 matches. Totally there are 3 mismatches
In case 2, I lost 2 characters (^ = loss of character compared to
reference sentence) -
TOMISAGOODBOY
T^MISAGOOD^OY (here I lost 2 characters) = I have 2 mismatches
TOMISAGOOODBOOY (here I have 2 extra characters O and O) = I have two
mismatches
In case 4: I have 42 matches, extra A and 19 matches = so I have 1
mismatch
How can that mismatch number from matches string.
1. I have to count how many A or T or G or C (believe me only these 4
letters will appear in this, i will not see Z or B or K etc)
2. ^T or ^A or ^G or ^C will also be a mismatch
desired output:
Length Matches mismatches
77 24A0T9T36 3
71 25^T9^T37 2
60 25^T9^T26 2
62 42A19 1
10 6^TTT1 3
I am sorry but I do not understand, and do not have the patience to wade
through all the above in the hopes of gaining insight.
Perhaps you could restate the problem in a way that makes it crystal clear.
--
Bob Gailer
919-636-4239
Chapel Hill NC
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