Primers in 2004

Programs such as MFOLD and ViennaRNA are widely used to predict RNA secondary structures. How do these algorithms work? Why can't they predict RNA pseudoknots? How accurate are they, and will they get better?

Statistical models called hidden Markov models are a recurring theme in computational biology. What are hidden Markov models, and why are they so useful for so many different problems?

There seem to be a lot of computational biology papers with 'Bayesian' in their titles these days. What's distinctive about 'Bayesian' methods?

Many sequence alignment programs use the BLOSUM62 score matrix to score pairs of aligned residues. Where did BLOSUM62 come from?

Sequence alignment methods often use something called a 'dynamic programming' algorithm. What is dynamic programming and how does it work?