Pairwise sequence alignment--it's all about us!

Pairwise alignment is one of the most fundamental tools of bioinformaticsand underpins a variety of other, more sophisticated methodsof annotation. Pairwise alignment in its most rigorous formuses a method called ‘dynamic programming’, whichis highly accurate, but also incredibly costly to compute. In order to align anything other than an exact alphabetic match,the algorithm has to know what it is looking for and how itcan evaluate the worth of what it finds. To this end, ‘comparisonmatrices’ have been created which define a score for everypossible match possibility—an effective tally of how wellthe computational alignment is doing. The software will searchfor the highest score available. The final score is relevantonly with its resulting alignment and cannot be used outsidethis context. In the case of DNA, comparison values