Transition/Transversion ratio

Question

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?

Answer 1

You are almost on the right path.

This schematics from Wikipedia is quite clear in my opinion.

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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.

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In your specific example, given the sequences

 ACGATG 
 TCAGTG

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).