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Constraint-based genetic compilation
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Ladroue, Christophe and Kalvala, Sara (2015) Constraint-based genetic compilation. In: Dediu, Adrian-Horia and Hernández-Quiroz, Francisco and Marin-Vide, Carlos and Rosenblueth, David A., (eds.) Algorithms for Computational Biology : Second International Conference, AlCoB 2015, Mexico City, Mexico, August 4-5, 2015, Proceedings. Lecture Notes in Computer Science, 9199 . Springer, pp. 25-38. ISBN 9783319212326
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Official URL: http://dx.doi.org/10.1007/978-3-319-21233-3_3
Abstract
Synthetic biology aims at facilitating the design of new organisms via the standardization of biological parts and following engineering principles. We present atgc (Assistant To Genetic Compilation), a software tool that automatically builds a functional sequence of DNA from a minimal set of requirements. Through a simple language, the user provides in-house knowledge about their construct (e.g. relative placement of parts, number of restriction enzymes). atgc combines information from established biology, user knowledge and bioinformatics databases, and maps the problem to a constraint satisfaction setting. The solution is a functional DNA sequence ready to be assembled and transferred to a target organism.
Item Type: | Book Item | ||||||
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Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QH Natural history > QH426 Genetics |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | ||||||
Library of Congress Subject Headings (LCSH): | Synthetic biology -- Research, Constraints (Artificial intelligence) , Genetic engineering, DNA | ||||||
Series Name: | Lecture Notes in Computer Science | ||||||
Publisher: | Springer | ||||||
ISBN: | 9783319212326 | ||||||
ISSN: | 0302-9743 | ||||||
Book Title: | Algorithms for Computational Biology : Second International Conference, AlCoB 2015, Mexico City, Mexico, August 4-5, 2015, Proceedings | ||||||
Editor: | Dediu, Adrian-Horia and Hernández-Quiroz, Francisco and Marin-Vide, Carlos and Rosenblueth, David A. | ||||||
Official Date: | 28 July 2015 | ||||||
Dates: |
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Volume: | 9199 | ||||||
Page Range: | pp. 25-38 | ||||||
DOI: | 10.1007/978-3-319-21233-3_3 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||
Date of first compliant deposit: | 23 February 2016 | ||||||
Date of first compliant Open Access: | 28 July 2016 | ||||||
Funder: | Engineering and Physical Sciences Research Council (EPSRC) | ||||||
Grant number: | EP/I03157X/1 | ||||||
Conference Paper Type: | Paper | ||||||
Title of Event: | Algorithms for Computational Biology, 2nd international conference | ||||||
Type of Event: | Conference | ||||||
Location of Event: | Mexico City | ||||||
Date(s) of Event: | 4-6 Aug 2015 |
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