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.