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Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Parallel Communicating Grammar Systems (SPCGS) has extended SCFG to model RNA pseudoknots. However, the alignment algorithm requires O(n 4 ) memory for a sequence of length n. In this paper, we develop a memory efficient algorithm for sequence-structure alignments including pseudoknots. This new algorithm reduces the memorydoi:10.1504/ijbra.2006.010606 pmid:18048167 fatcat:ggxwyhsghrbrvotlzhbmpo4tty