Recent methods for rna modeling using stochastic context-free grammars

Yasubumi Sakakibara; Michael Brown; Richard Hughey; Saira Mian; Kimmen Sjölander; Rebecca C. Underwood; David Haussler

doi:10.1007/3-540-58094-8_25

Recent methods for rna modeling using stochastic context-free grammars

Yasubumi Sakakibara, Michael Brown, Richard Hughey, Saira Mian, Kimmen Sjölander, Rebecca C. Underwood, David Haussler

研究成果: Conference contribution

16 被引用数 (Scopus)

抄録

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.

本文言語	English
ホスト出版物のタイトル	Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings
編集者	Maxime Crochemore, Dan Gusfield
出版社	Springer Verlag
ページ	290-306
ページ数	17
ISBN（印刷版）	9783540580942
DOI	https://doi.org/10.1007/3-540-58094-8_25
出版ステータス	Published - 1994 1 1
外部発表	はい
イベント	5th Annual Symposium on Combinatorial Pattern Matching, CPM 1994 - Asilomar, United States 継続期間: 1994 6 5 → 1994 6 8

出版物シリーズ

名前	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
巻	807 LNCS
ISSN（印刷版）	0302-9743
ISSN（電子版）	1611-3349

Other

Other	5th Annual Symposium on Combinatorial Pattern Matching, CPM 1994
Country	United States
City	Asilomar
Period	94/6/5 → 94/6/8

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

文献へのアクセス

10.1007/3-540-58094-8_25

フィンガープリント「Recent methods for rna modeling using stochastic context-free grammars」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル

Sakakibara, Y., Brown, M., Hughey, R., Mian, S., Sjölander, K., Underwood, R. C., & Haussler, D. (1994). Recent methods for rna modeling using stochastic context-free grammars. In M. Crochemore, & D. Gusfield (Eds.), Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings (pp. 290-306). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 807 LNCS). Springer Verlag. https://doi.org/10.1007/3-540-58094-8_25

Recent methods for rna modeling using stochastic context-free grammars. / Sakakibara, Yasubumi; Brown, Michael; Hughey, Richard; Mian, Saira; Sjölander, Kimmen; Underwood, Rebecca C.; Haussler, David.

Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. ed. / Maxime Crochemore; Dan Gusfield. Springer Verlag, 1994. p. 290-306 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 807 LNCS).

研究成果: Conference contribution

Sakakibara, Y, Brown, M, Hughey, R, Mian, S, Sjölander, K, Underwood, RC & Haussler, D 1994, Recent methods for rna modeling using stochastic context-free grammars. in M Crochemore & D Gusfield (eds), Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 807 LNCS, Springer Verlag, pp. 290-306, 5th Annual Symposium on Combinatorial Pattern Matching, CPM 1994, Asilomar, United States, 94/6/5. https://doi.org/10.1007/3-540-58094-8_25

Sakakibara Y, Brown M, Hughey R, Mian S, Sjölander K, Underwood RC et al. Recent methods for rna modeling using stochastic context-free grammars. In Crochemore M, Gusfield D, editors, Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. Springer Verlag. 1994. p. 290-306. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/3-540-58094-8_25

Sakakibara, Yasubumi ; Brown, Michael ; Hughey, Richard ; Mian, Saira ; Sjölander, Kimmen ; Underwood, Rebecca C. ; Haussler, David. / Recent methods for rna modeling using stochastic context-free grammars. Combinatorial Pattern Matching - 5th Annual Symposium, CPM 1994, Proceedings. editor / Maxime Crochemore ; Dan Gusfield. Springer Verlag, 1994. pp. 290-306 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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