Speeding up Parsing of Biological Context-Free Grammars

Grammars have been shown to be a very useful way to model biological sequences families. As both the quantity of biological sequences and the complexity of the biological grammars increase, generic and efficient methods for parsing are needed. We consider two parsers for context-free grammars: depth-first top-down parser and chart parser; we analyse and compare them, both theoretically and empirically, with respect to biological data. The theoretical comparison is based on a common feature of biological grammars: the gap – a gap is an element of the grammars designed to match any subsequence of the parsed string. The empirical comparison is based on grammars and sequences used by the bioinformatics community. Our conclusions are that: (1) the chart parsing algorithm is significantly faster than the depth-first top-down algorithm, (2) designing special treatments in the algorithms for managing gaps is useful, and (3) the way the grammar encodes gaps has to be carefully chosen, when using parsers not optimised for managing gaps, to prevent important increases in running times.