Nucleotide and amino acids?

Question

I would like to have some more information on the following subject, My question is about the nucleotide and amino acid sequences. If you have two suspected viruses in two different strains animals and one of them is sequenced and the second one is not.

If you would like to know the similarity and the different in nucleotide and in amino acids, what are the procedures? at the same time, what will be the impact if the amino acids of the two viruses are similar and the nucleotides are different.

Answer 1

First you need to sequence the second virus. I won't explain that in detail, other than to say that if you know the sequence of the first virus and you suspect that the second virus is related you can use the sequence of the first virus to make PCR primers, which you can then use to generate template DNA for sequencing.

Second, you align the nucleotide sequences of the two viruses, and you align the amino acid sequences of the two viruses. This will tell you similarity levels.

If the amino acids are very similar, and the nucleotides diverge significantly (are very different), this is evidence of negative selection on the viral populations. Many viruses make lots of mutations when they replicate, which explains the changes at the nucleotide level. However, if there is strong selection pressure for a specific type of protein most or all viruses that have mutations affecting amino acid sequence will be selected out of the population (this is negative selection). Most of your mutations end up being in wobble positions, silent mutations.