TY - GEN
T1 - Recent methods for rna modeling using stochastic context-free grammars
AU - Sakakibara, Yasubumi
AU - Brown, Michael
AU - Hughey, Richard
AU - Mian, Saira
AU - Sjölander, Kimmen
AU - Underwood, Rebecca C.
AU - Haussler, David
PY - 1994/1/1
Y1 - 1994/1/1
N2 - Stochastic context-free grammars (SC, FGs) Call be applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture tile sequences’ common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. This paper discusses our new algorithm, Tree-Grammar EM, for deducing SCFG parameters automatically from unaligned, unfolded training sequences. Tree-Grammar EM, a generalization of tile HMM forward-backward algorithm, is based on tree grammars and is faster than tile previously proposed inside-outside SCFG training algorithm. Independently, Scan Eddy and Richard Durbin have introduced a trainable “covariance model” (CM) to perform similar tasks. We compare and contrast our methods with theirs.
AB - Stochastic context-free grammars (SC, FGs) Call be applied to the problems of folding, aligning and modeling families of homologous RNA sequences. SCFGs capture tile sequences’ common primary and secondary structure and generalize the hidden Markov models (HMMs) used in related work on protein and DNA. This paper discusses our new algorithm, Tree-Grammar EM, for deducing SCFG parameters automatically from unaligned, unfolded training sequences. Tree-Grammar EM, a generalization of tile HMM forward-backward algorithm, is based on tree grammars and is faster than tile previously proposed inside-outside SCFG training algorithm. Independently, Scan Eddy and Richard Durbin have introduced a trainable “covariance model” (CM) to perform similar tasks. We compare and contrast our methods with theirs.
UR - http://www.scopus.com/inward/record.url?scp=85015182436&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85015182436&partnerID=8YFLogxK
U2 - 10.1007/3-540-58094-8_25
DO - 10.1007/3-540-58094-8_25
M3 - Conference contribution
AN - SCOPUS:85015182436
SN - 9783540580942
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 290
EP - 306
BT - Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings
A2 - Crochemore, Maxime
A2 - Gusfield, Dan
PB - Springer Verlag
T2 - 5th Annual Symposium on Combinatorial Pattern Matching, CPM 1994
Y2 - 5 June 1994 through 8 June 1994
ER -