Depth-first search encoding of RNA substructures

Qingfeng Chen; Chaowang Lan; Jinyan Li; Baoshan Chen; Lusheng Wang; Chengqi Zhang

doi:10.1007/978-3-319-42291-6_32

Depth-first search encoding of RNA substructures

Qingfeng Chen^*, Chaowang Lan, Jinyan Li, Baoshan Chen, Lusheng Wang, Chengqi Zhang

^*Corresponding author for this work

Department of Computer Science

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

Abstract

RNA structural motifs are important in RNA folding process. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is underdeveloped owing to varied and unnormalized substructures. This prevents us from understanding RNAs functions. This article proposes a DFS (depth-first search) encoding for RNA substructures. The results show that our methods are useful in modelling complex RNA secondary structures.

Original language	English
Title of host publication	Intelligent Computing Theories and Application
Subtitle of host publication	12th International Conference, ICIC 2016, Proceedings
Editors	Prashan Premaratne, De-Shuang Huang, Vitoantonio Bevilacqua
Publisher	Springer Verlag
Pages	328-334
Volume	9771
ISBN (Print)	9783319422909
DOIs	https://doi.org/10.1007/978-3-319-42291-6_32
Publication status	Published - 2016
Event	12th International Conference on Intelligent Computing Theories and Application, ICIC 2016 - Lanzhou, China Duration: 2 Aug 2016 → 5 Aug 2016

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9771
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	12th International Conference on Intelligent Computing Theories and Application, ICIC 2016
Place	China
City	Lanzhou
Period	2/08/16 → 5/08/16

Research Keywords

Data mining
RNA
Subgraph
Substructure
Support

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10.1007/978-3-319-42291-6_32

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Chen, Q., Lan, C., Li, J., Chen, B., Wang, L., & Zhang, C. (2016). Depth-first search encoding of RNA substructures. In P. Premaratne, D.-S. Huang, & V. Bevilacqua (Eds.), Intelligent Computing Theories and Application: 12th International Conference, ICIC 2016, Proceedings (Vol. 9771, pp. 328-334). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9771). Springer Verlag. https://doi.org/10.1007/978-3-319-42291-6_32

Chen, Qingfeng ; Lan, Chaowang ; Li, Jinyan et al. / Depth-first search encoding of RNA substructures. Intelligent Computing Theories and Application: 12th International Conference, ICIC 2016, Proceedings. editor / Prashan Premaratne ; De-Shuang Huang ; Vitoantonio Bevilacqua. Vol. 9771 Springer Verlag, 2016. pp. 328-334 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Depth-first search encoding of RNA substructures",

abstract = "RNA structural motifs are important in RNA folding process. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is underdeveloped owing to varied and unnormalized substructures. This prevents us from understanding RNAs functions. This article proposes a DFS (depth-first search) encoding for RNA substructures. The results show that our methods are useful in modelling complex RNA secondary structures.",

keywords = "Data mining, RNA, Subgraph, Substructure, Support",

author = "Qingfeng Chen and Chaowang Lan and Jinyan Li and Baoshan Chen and Lusheng Wang and Chengqi Zhang",

year = "2016",

doi = "10.1007/978-3-319-42291-6_32",

language = "English",

isbn = "9783319422909",

volume = "9771",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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pages = "328--334",

editor = "Prashan Premaratne and De-Shuang Huang and Vitoantonio Bevilacqua",

booktitle = "Intelligent Computing Theories and Application",

address = "Germany",

note = "12th International Conference on Intelligent Computing Theories and Application, ICIC 2016 ; Conference date: 02-08-2016 Through 05-08-2016",

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Chen, Q, Lan, C, Li, J, Chen, B, Wang, L & Zhang, C 2016, Depth-first search encoding of RNA substructures. in P Premaratne, D-S Huang & V Bevilacqua (eds), Intelligent Computing Theories and Application: 12th International Conference, ICIC 2016, Proceedings. vol. 9771, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9771, Springer Verlag, pp. 328-334, 12th International Conference on Intelligent Computing Theories and Application, ICIC 2016, Lanzhou, China, 2/08/16. https://doi.org/10.1007/978-3-319-42291-6_32

Depth-first search encoding of RNA substructures. / Chen, Qingfeng; Lan, Chaowang; Li, Jinyan et al.
Intelligent Computing Theories and Application: 12th International Conference, ICIC 2016, Proceedings. ed. / Prashan Premaratne; De-Shuang Huang; Vitoantonio Bevilacqua. Vol. 9771 Springer Verlag, 2016. p. 328-334 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9771).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - Depth-first search encoding of RNA substructures

AU - Chen, Qingfeng

AU - Lan, Chaowang

AU - Li, Jinyan

AU - Chen, Baoshan

AU - Wang, Lusheng

AU - Zhang, Chengqi

PY - 2016

Y1 - 2016

N2 - RNA structural motifs are important in RNA folding process. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is underdeveloped owing to varied and unnormalized substructures. This prevents us from understanding RNAs functions. This article proposes a DFS (depth-first search) encoding for RNA substructures. The results show that our methods are useful in modelling complex RNA secondary structures.

AB - RNA structural motifs are important in RNA folding process. Traditional index-based and shape-based schemas are useful in modeling RNA secondary structures but ignore the structural discrepancy of individual RNA family member. Further, the in-depth analysis of underlying substructure pattern is underdeveloped owing to varied and unnormalized substructures. This prevents us from understanding RNAs functions. This article proposes a DFS (depth-first search) encoding for RNA substructures. The results show that our methods are useful in modelling complex RNA secondary structures.

KW - Data mining

KW - RNA

KW - Subgraph

KW - Substructure

KW - Support

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U2 - 10.1007/978-3-319-42291-6_32

DO - 10.1007/978-3-319-42291-6_32

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9783319422909

VL - 9771

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 328

EP - 334

BT - Intelligent Computing Theories and Application

A2 - Premaratne, Prashan

A2 - Huang, De-Shuang

A2 - Bevilacqua, Vitoantonio

PB - Springer Verlag

T2 - 12th International Conference on Intelligent Computing Theories and Application, ICIC 2016

Y2 - 2 August 2016 through 5 August 2016

ER -

Chen Q, Lan C, Li J, Chen B, Wang L, Zhang C. Depth-first search encoding of RNA substructures. In Premaratne P, Huang DS, Bevilacqua V, editors, Intelligent Computing Theories and Application: 12th International Conference, ICIC 2016, Proceedings. Vol. 9771. Springer Verlag. 2016. p. 328-334. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-42291-6_32

Depth-first search encoding of RNA substructures

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