GCG: Pattern Recognition

Pattern recognition in biological data is difficult to achieve. On the one hand, it is simple trying to find information based on identity of patterns described in a search string. Method 1 and 2 describe such a pattern search for text strings. More sophisticated searches use a pattern definition language (e.g., method 6 and 7 ), whereas a different approach just counts given patterns and plots or tabulates the result (method 3 and 4 ). Another method of pattern recognition is to try to find repeats in a given sequence, which is basically the pattern and search with patterns to be found by the program itself (method 8 ). Note that searching for a reading frame also uses pattern searching methods (in the most simple case, just by detection of ATG), but this kind of pattern search is described in Chapter 11 . Similarly, sequence searching with profiles, which is described in Chapter 9 , is also a kind of pattern search not listed here.