TY - GEN
T1 - Stochastic context-free grammars for modeling RNA
AU - Sakakibara, Yasubumi
AU - Brown, Michael
AU - Underwood, Rebecca C.
AU - Mian, I. Saira
AU - Haussler, David
PY - 1995/1/1
Y1 - 1995/1/1
N2 - Stochastic context-free grammars (SCFGs) are used to fold, align and model a family of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. The novel aspect of this work is that SCFG parameters are learned automatically from unaligned, unfolded training sequences. A generalization of the HMM forward-backward algorithm is introduced. The new algorithm, based on tree grammars and faster than the previously proposed SCFG inside-outside algorithm, is tested on the transfer RNA (tRNA) family. Results show the model can discern tRNA from similar-length RNA sequences, can find secondary structure of new tRNA sequences, and can give multiple alignments of large sets of tRNA sequences. The model is extended to handle introns in tRNA.
AB - Stochastic context-free grammars (SCFGs) are used to fold, align and model a family of homologous RNA sequences. SCFGs capture the sequences' common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. The novel aspect of this work is that SCFG parameters are learned automatically from unaligned, unfolded training sequences. A generalization of the HMM forward-backward algorithm is introduced. The new algorithm, based on tree grammars and faster than the previously proposed SCFG inside-outside algorithm, is tested on the transfer RNA (tRNA) family. Results show the model can discern tRNA from similar-length RNA sequences, can find secondary structure of new tRNA sequences, and can give multiple alignments of large sets of tRNA sequences. The model is extended to handle introns in tRNA.
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M3 - Conference contribution
AN - SCOPUS:0028907514
SN - 0818650907
T3 - Proceedings of the Hawaii International Conference on System Sciences
SP - 284
EP - 293
BT - Proceedings of the Hawaii International Conference on System Sciences
A2 - Nunamaker, Jay F.
A2 - Sprague, Ralph H.Jr.
PB - Publ by IEEE
T2 - Proceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5)
Y2 - 4 January 1994 through 7 January 1994
ER -