String Play with Regular Expressions
Mark D. LeBlanc, Betsey Dexter Dyer · Oxford University Press eBooks · 2007
This chapter describes some hurdles, which can be overcome, so that the pattern matching syntax of regular expressions (‘regex’) can be used immediately. It also presents some surprisingly relevant word play. Almost all DNA sequence analysis is a form of pattern matching. Whether one compares sequences to build phylogenetic trees or to determine their identities, similar patterns are looked for. Many different programming languages use regex's but they fit especially well within Perl's syntax. Facing page translations are often used to help with the translation between two different languages, e.g. English text on the left-hand, even numbered pages and the comparable French text on the right-hand odd numbered pages. The chapter introduces regular expressions syntax in small doses, first applying regex to English text on the left and then applying that same regex to DNA sequences on the right-hand page. Side boxes include Alice Kober and Why search for repeats?