Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots

Małgorzata Nowicka; Vinay K. Gautam; Pekka Orponen

doi:10.1007/978-3-031-63742-1_14

Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots

Małgorzata Nowicka, Vinay K. Gautam, Pekka Orponen^*

^*Tämän työn vastaava kirjoittaja

Norwegian University of Science and Technology

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference article in proceedings › Scientific › vertaisarvioitu

Abstrakti

We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will determine one in time which is essentially linear in the size of the textual description. (That is, except for a final stochastic fine-tuning step.) If a planar rendering is not possible, the method will compute a visually pleasing approximate rendering in quadratic time. Examples of diagrams produced by the method are presented in the paper.

Alkuperäiskieli	Englanti
Otsikko	Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings
Toimittajat	Da-Jung Cho, Jongmin Kim
Kustantaja	Springer
Sivut	190-202
Sivumäärä	13
ISBN (elektroninen)	978-3-031-63742-1
ISBN (painettu)	978-3-031-63741-4
DOI - pysyväislinkit	https://doi.org/10.1007/978-3-031-63742-1_14
Tila	Julkaistu - 2024
OKM-julkaisutyyppi	A4 Artikkeli konferenssijulkaisussa
Tapahtuma	International Conference on Unconventional Computation and Natural Computation - Pohang, Etelä-Korea Kesto: 17 kesäk. 2024 → 21 kesäk. 2024 Konferenssinumero: 21

Julkaisusarja

Nimi	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Kustantaja	Springer
Vuosikerta	14776 LNCS
ISSN (painettu)	0302-9743
ISSN (elektroninen)	1611-3349

Conference

Conference	International Conference on Unconventional Computation and Natural Computation
Lyhennettä	UCNC
Maa/Alue	Etelä-Korea
Kaupunki	Pohang
Ajanjakso	17/06/2024 → 21/06/2024

Pääsy asiakirjaan

10.1007/978-3-031-63742-1_14

https://arxiv.org/abs/2308.06392

Muut tiedostot ja linkit

Linkki julkaisuun Scopuksessa

Siteeraa tätä

Nowicka, M., Gautam, V. K., & Orponen, P. (2024). Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. teoksessa D.-J. Cho, & J. Kim (Toimittajat), Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings (Sivut 190-202). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vuosikerta 14776 LNCS). Springer. https://doi.org/10.1007/978-3-031-63742-1_14

Nowicka, Małgorzata ; Gautam, Vinay K. ; Orponen, Pekka. / Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Toimittaja / Da-Jung Cho ; Jongmin Kim. Springer, 2024. Sivut 190-202 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots",

abstract = "We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will determine one in time which is essentially linear in the size of the textual description. (That is, except for a final stochastic fine-tuning step.) If a planar rendering is not possible, the method will compute a visually pleasing approximate rendering in quadratic time. Examples of diagrams produced by the method are presented in the paper.",

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author = "Ma{\l}gorzata Nowicka and Gautam, {Vinay K.} and Pekka Orponen",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.; International Conference on Unconventional Computation and Natural Computation, UCNC ; Conference date: 17-06-2024 Through 21-06-2024",

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Nowicka, M, Gautam, VK & Orponen, P 2024, Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. julkaisussa D-J Cho & J Kim (toim), Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vuosikerta 14776 LNCS, Springer, Sivut 190-202, International Conference on Unconventional Computation and Natural Computation, Pohang, Etelä-Korea, 17/06/2024. https://doi.org/10.1007/978-3-031-63742-1_14

Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. / Nowicka, Małgorzata; Gautam, Vinay K.; Orponen, Pekka.
Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. toim. / Da-Jung Cho; Jongmin Kim. Springer, 2024. s. 190-202 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vuosikerta 14776 LNCS).

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussa › Conference article in proceedings › Scientific › vertaisarvioitu

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N2 - We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will determine one in time which is essentially linear in the size of the textual description. (That is, except for a final stochastic fine-tuning step.) If a planar rendering is not possible, the method will compute a visually pleasing approximate rendering in quadratic time. Examples of diagrams produced by the method are presented in the paper.

AB - We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will determine one in time which is essentially linear in the size of the textual description. (That is, except for a final stochastic fine-tuning step.) If a planar rendering is not possible, the method will compute a visually pleasing approximate rendering in quadratic time. Examples of diagrams produced by the method are presented in the paper.

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KW - DSD systems

KW - graph drawing

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KW - visualisation

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Nowicka M, Gautam VK, Orponen P. Automated Rendering of Multi-stranded DNA Complexes with Pseudoknots. julkaisussa Cho DJ, Kim J, toimittajat, Unconventional Computation and Natural Computation - 21st International Conference, UCNC 2024, Proceedings. Springer. 2024. s. 190-202. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-031-63742-1_14