[Tutor] number of mismatches in a string
ilhs_hs at yahoo.com
Fri Mar 2 20:11:30 CET 2012
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.
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) -
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
Length Matches mismatches
77 24A0T9T36 3
71 25^T9^T37 2
60 25^T9^T26 2
62 42A19 1
10 6^TTT1 3
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