Next generation sequencing offers a lot of extremely interesting opportunities, but it also presents us with at least as many difficulties – especially when you are working with ancient DNA. I have already touched upon the problem of primer contamination in the data in a previous post. Here, I want to mention a few problems with PCR artifacts.

If you want to predict the secondary structure – i.e. the basepairing interactions – for a single RNA sequence, you would normally rely on energy parameters and try to find the minimum free energy structure. If, however, you have multiple related sequences you suddenly have access to all the evolutionary information you get from a multiple alignment. This can be utilized.

An introduction to the field of promoter analysis. This post mainly focus on motif-searching and different strategies for assessment of functional of detected sites.