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Tools for Molecular Biology

1. Calculate the degree of degeneracy
(By courtesy of Dr. Mitsuo Iwadate, Dept. Biological Sciences)

The degeneracy of the primer is the number of unique sequence combinations it contains.
　　ex) A primer, 5'-AAGCTTRCCBNGAGC-3' contains 3 mixed bases,
　　　R (A or G), B (G or T or C), and N (A or T or G or C).
　　　In this case 2*3*4=24, represents the number of different primer sequences.

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2. Find suitable regions for PCR primers from the template
(By courtesy of Dr. Mitsuo Iwadate and Mr. Wataru Sato, Dept. Biological Sciences)

This program calculates the Tm plot of every n-mer (the default is a 21-mer) of the template sequence.
The graph shows values calculated using the Wallace method, the nearest neighbor method, and the %GC method.

　・When the Tm for primers are too high/too low, you will get no good results.
　　Primers with appropriate Tm are necessary for a successful PCR.
　・Primers with the Tm plot value of its 3' end slightly higher than that of 5' end, will stably bind to the template.
　　Such primers should work well for general PCR or dye terminator sequencing.
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