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I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time to ask questions or go over examples. One topic is transition/transversion ratio, and I'm not 100% sure I'm understanding it. Do you just compare the first symbol of string 1 to the first symbol of string 2? What if the two symbols you're comparing are the same? Do you just ignore it? Let's say string 1 is ACGATG and string 2 is TCAGTG. Would the ratio be 2/1?

Here are the comparisons I made. Transitions: G-->A, A-->G, Transversions: A-->T, Neither: C-->C, T-->T, G-->G

Is this correct or am I completely on the wrong path?

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up vote 1 down vote accepted

You are almost on the right path.

This schematics from Wikipedia is quite clear in my opinion.

Transitions and transversions

Slightly more chemical explanation (which you do not necessarily need to do bioinformatics, however I think it is always better to know exactly what you are dealing with outside of the computer!)

The idea is that you have four basic nucleotides: cytosine and thymine are called pyrymidines and adenine (A) and guanine (G) which are called purines. Pyrymidines are characterised by a 6 carbon azo-ring which is called a pyridine, while purines have a larger double ring, formed by a pyridine ring + an imidazole ring.

A transition is defined as the passage purine -> purine or pyrimidine -> pyrimidine.
A transversion is the passage purine -> pyrimidine, or viceversa.

These mutations can be caused for instance by certain chemicals, such as alkylating agents, or by ionizing radiations.

In your specific example, given the sequences


You have 3 mutations:

A -> T  
G -> A
A -> G

So you have 1 transversion (from the purine A to the pyrimidine T) and two transitions (between the purines A and G).

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Thanks! That's pretty much what I thought, but nice to get confirmation. – Brett Feb 1 '14 at 17:41

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